bamdata_Developmental_transcriptome.xml

<?xml version="1.0" encoding="UTF-8"?>
	<files xmltitle="Developmental transcriptome - Klepikova et al" author="Anna V. Klepikova, Artem S. Kasianov, Evgeny S. Gerasimov, Maria D. Logacheva, Aleksey A. Penin" contact="">

		<file info="IN.sn, First elongated internode (from last rosette leaf to first cauline leaf). Sample was collected when first silique was yellow and ready to open." record_number="SRR3581899" foreground="0B539C" hex_colour="0x0b539c" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581899/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33820866" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Internode.svg" description="Arabidopsis thaliana Senescent internode" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581899" species="Arabidopsis thaliana">
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		<file info="SL.sn2, Whole senescent silique 2. Sample was collected when first silique was yellow and ready to open." record_number="SRR3581898" foreground="937326" hex_colour="0x937326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581898/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29627136" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique1-5.svg" description="Arabidopsis thaliana Senescent silique 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581898" species="Arabidopsis thaliana">
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		<file info="POD.sn1, Pod of the senescent silique 1. Sample was collected when first silique was yellow and ready to open." record_number="SRR3581897" foreground="929326" hex_colour="0x929326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581897/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29447531" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the senescent silique 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581897" species="Arabidopsis thaliana">
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		<file info="SD.sn1, Seeds from the senescent silique 1. Sample was collected when first silique was yellow and ready to open." record_number="SRR3581896" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581896/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="36088816" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Seeds from the senescent silique 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581896" species="Arabidopsis thaliana">
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		<file info="SD.g3, Seeds at third day after soaking." record_number="SRR3581895" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581895/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33224602" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-GerminatingSeed.svg" description="Arabidopsis thaliana Germinating seeds 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581895" species="Arabidopsis thaliana">
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		<file info="SD.g2, Seeds at second day after soaking." record_number="SRR3581894" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581894/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="41118826" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-GerminatingSeed.svg" description="Arabidopsis thaliana Germinating seeds 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581894" species="Arabidopsis thaliana">
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		<file info="SD.g1, Seeds at first day after soaking." record_number="SRR3581893" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581893/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="48479083" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-GerminatingSeed.svg" description="Arabidopsis thaliana Germinating seeds 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581893" species="Arabidopsis thaliana">
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		<file info="SD.d, Dry seeds." record_number="SRR3581892" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581892/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29133506" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Dry Seeds" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581892" species="Arabidopsis thaliana">
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		<file info="POD.y6-7, Pistils of 6th and 7th flowers (before pollination), ovules and stigma removed. Sample collected at the moment of the abscission of the first flower." record_number="SRR3581891" foreground="E7FF65" hex_colour="0xe7ff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581891/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26385752" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="carpels" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Carpel of 6th and 7th flowers" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581891" species="Arabidopsis thaliana">
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		<file info="STI, Stigmatic tissue from pistils of 6th and 7th flowers (before pollination). Sample collected at the moment of the abscission of the first flower." record_number="SRR3581890" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581890/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="30997938" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="Stigma_tissue" svgname="ath-StigmaAndOvaries.svg" description="Arabidopsis thaliana Stigmatic tissue" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581890" species="Arabidopsis thaliana">
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		<file info="OV.y6-7, Ovules from 6th and 7th flowers (before pollination). Sample collected at the moment of the abscission of the first flower." record_number="SRR3581889" foreground="CCFF65" hex_colour="0xccff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581889/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27509175" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="Ovary_tissue" svgname="ath-StigmaAndOvaries.svg" description="Arabidopsis thaliana Ovules from 6th and 7th flowers" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581889" species="Arabidopsis thaliana">
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		<file info="SD.y5, Seeds from silique 5. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581888" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581888/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29692016" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed1-4.svg" description="Arabidopsis thaliana Young seeds 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581888" species="Arabidopsis thaliana">
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		<file info="SD.y4, Seeds from silique 4. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581887" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581887/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33047842" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Young seeds 4" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581887" species="Arabidopsis thaliana">
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		<file info="SD.y3, Seeds from silique 3. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581886" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581886/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="30262908" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Young seeds 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581886" species="Arabidopsis thaliana">
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		<file info="SD.y2, Seeds from silique 2. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581885" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581885/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26871995" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Young seeds 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581885" species="Arabidopsis thaliana">
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		<file info="SD.y1, Seeds from silique 1. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581884" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581884/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="30130352" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Young seeds 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581884" species="Arabidopsis thaliana">
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		<file info="SL8, Whole silique 8. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581883" foreground="818211" hex_colour="0x818211" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581883/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="38597480" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique6-10.svg" description="Arabidopsis thaliana Silique 8" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581883" species="Arabidopsis thaliana">
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		<file info="POD7, Pod of the silique 7 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581882" foreground="B2B42A" hex_colour="0xb2b42a" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581882/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="30923021" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 7" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581882" species="Arabidopsis thaliana">
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		<file info="SD7, Seeds from silique 7. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581881" foreground="FECC00" hex_colour="0xfecc00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581881/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="38167977" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed1-4.svg" description="Arabidopsis thaliana Seeds 7" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581881" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
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		<file info="SL6, Whole silique 6. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581880" foreground="818211" hex_colour="0x818211" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581880/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="37913237" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique6-10.svg" description="Arabidopsis thaliana Silique 6" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581880" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="POD5, Pod of the silique 5 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581879" foreground="B2B42A" hex_colour="0xb2b42a" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581879/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="34607498" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581879" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
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		<file info="SD5, Seeds from silique 5. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581878" foreground="FECC00" hex_colour="0xfecc00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581878/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="38743274" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Seeds 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581878" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="SL4, Whole silique 4. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581877" foreground="937326" hex_colour="0x937326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581877/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="32752222" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique1-5.svg" description="Arabidopsis thaliana Silique 4" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581877" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="POD3, Pod of the silique 3 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581876" foreground="929326" hex_colour="0x929326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581876/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="42213450" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581876" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
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		<file info="SD3, Seeds from silique 3. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581875" foreground="FE9900" hex_colour="0xfe9900" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581875/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="54392355" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Seeds 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581875" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="SL2, Whole silique 2. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581874" foreground="937326" hex_colour="0x937326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581874/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="42315008" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique1-5.svg" description="Arabidopsis thaliana Silique 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581874" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="POD1, Pod of the silique 1 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581873" foreground="929326" hex_colour="0x929326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581873/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="37787924" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581873" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
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		<file info="SD1, Seeds from silique 1. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581872" foreground="FE9900" hex_colour="0xfe9900" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581872/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="36316453" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Seeds 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581872" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
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		<file info="IN, First elongated internode (from last rosette leaf to first cauline leaf). All samples are collected at the moment of the anthesis of the first flower." record_number="SRR3581871" foreground="99CCFF" hex_colour="0x99ccff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581871/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24067897" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Internode.svg" description="Arabidopsis thaliana Internode" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581871" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="AX, Axis of the inflorescence without flowers and pedicels. All samples are collected at the moment of the anthesis of the first flower." record_number="SRR3581870" foreground="979999" hex_colour="0x979999" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581870/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23648130" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-ShootApexInflorescense.svg" description="Arabidopsis thaliana Axis of the inflorescence" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581870" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="PED, Pedicel of the first flower. All samples are collected at the moment of the anthesis of the first flower." record_number="SRR3581869" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581869/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33610537" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="receptacle" svgname="ath-Flower.svg" description="Arabidopsis thaliana Pedicel" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581869" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="F19+, Whole inflorescence apex from flower 19 to meristem. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581868" foreground="FFFF66" hex_colour="0xffff66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581868/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26920107" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart19" svgname="ath-FlowerDevelopment19.svg" description="Arabidopsis thaliana Flowers 19 and following" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581868" species="Arabidopsis thaliana">
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		<file info="F15-18, Whole flowers 15, 16, 17 and 18 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581867" foreground="FFFF66" hex_colour="0xffff66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581867/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23920075" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart15" svgname="ath-FlowerDevelopment15-18.svg" description="Arabidopsis thaliana Flowers 15-18" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581867" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F12-14, Whole flowers 12, 13 and 14 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581866" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581866/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25993357" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart12" svgname="ath-FlowerDevelopment12-14.svg" description="Arabidopsis thaliana Flowers 12-14" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581866" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F9-11, Whole flowers 9, 10 and 11 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581865" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581865/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27890271" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart9" svgname="ath-FlowerDevelopment9-11.svg" description="Arabidopsis thaliana Flowers 9-11" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581865" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F6-8, Whole flowers 6, 7 and 8 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581864" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581864/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23629111" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart6" svgname="ath-FlowerDevelopment6-8.svg" description="Arabidopsis thaliana Flowers 6-8" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581864" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F5, Whole flower 5 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581863" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581863/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27812173" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart5" svgname="ath-FlowerDevelopment5.svg" description="Arabidopsis thaliana Flower 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581863" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F4, Whole flower 4 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581862" foreground="D3D332" hex_colour="0xd3d332" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581862/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24940541" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart4" svgname="ath-FlowerDevelopment4.svg" description="Arabidopsis thaliana Flower 4" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581862" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F3, Whole flower 3 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581861" foreground="D3D332" hex_colour="0xd3d332" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581861/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26302127" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart3" svgname="ath-FlowerDevelopment3.svg" description="Arabidopsis thaliana Flower 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581861" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F2, Whole flower 2 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581860" foreground="CBCB32" hex_colour="0xcbcb32" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581860/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24522542" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flower" svgname="ath-Flower.svg" description="Arabidopsis thaliana Flower 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581860" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F1, Whole flower 1 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581859" foreground="CBCB32" hex_colour="0xcbcb32" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581859/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26101059" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flower" svgname="ath-Flower.svg" description="Arabidopsis thaliana Flower 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581859" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.SP.y, Sepals of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581858" foreground="CCFF65" hex_colour="0xccff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581858/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24481696" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="sepals" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Sepals of the young flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581858" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.AN.y, Anthers of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581857" foreground="FF5D5D" hex_colour="0xff5d5d" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581857/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33456560" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="anthers" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Anthers of the young flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581857" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.CA.y, Pistil of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581856" foreground="CCFF65" hex_colour="0xccff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581856/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28462107" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="carpels" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Carpels of the young flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581856" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.SP.ad, Sepals of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581855" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581855/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27712289" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="sepals" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Sepals of the mature flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581855" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.PT.ad, Petals of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581854" foreground="CBCB32" hex_colour="0xcbcb32" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581854/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26328598" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petals" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Petals of the mature flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581854" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.FM.ad, Filaments of stamens of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581853" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581853/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="34931944" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="filament" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Stamen filaments of the mature flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581853" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.AN.ad, Anthers of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581852" foreground="FF5D5D" hex_colour="0xff5d5d" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581852/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24049129" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="anthers" svgname="ath-Stamen.svg" description="Anthers of the mature flower (F.AN.ad)" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581852" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.CA.ad, Pistil of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581851" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581851/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27380567" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="carpels" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Carpels of the mature flower (before pollination)" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581851" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.AN, Anthers of first flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581850" foreground="FF0000" hex_colour="0xff0000" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581850/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28863066" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="anthers" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Opened Anthers" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581850" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.VN.sn, Midrib of the third leaf. Sample was collected when first silique was completely mature and nearly opened. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581849" foreground="0B539C" hex_colour="0x0b539c" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581849/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="31496414" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="veins" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Vein of the senescent leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581849" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.sn, Petiole of the third leaf. Sample was collected when first silique was completely mature and nearly opened. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581848" foreground="0B539C" hex_colour="0x0b539c" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581848/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27567816" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole of the senescent leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581848" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.lg, Whole third leaf. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581847" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581847/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28419567" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="leaf" svgname="ath-leaf.svg" description="Arabidopsis thaliana Leaf, mature" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581847" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.lg, Parts of the leaf blade without veins. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581846" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581846/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26604761" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina of the mature leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581846" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.VN.lg, Midrib of the third leaf. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581845" foreground="007EFF" hex_colour="0x007eff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581845/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24281268" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="veins" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Vein of the mature leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581845" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.lg, Petiole of the third leaf. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581844" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581844/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28702818" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole of the mature leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581844" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.i2, Parts of the leaf blade without veins. Sample was collected at 12th day after germination (10 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581843" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581843/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25091894" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina, intermediate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581843" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.VN.i2, Midrib of the third leaf. Sample was collected at 12th day after germination (10 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581842" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581842/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23473731" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="veins" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Vein, intermediate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581842" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.i2, Petiole of third leaf. Sample was collected at 12th day after germination (10 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581841" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581841/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24977332" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole, intermediate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581841" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.i1, Leaf blade of the third leaf. Sample was harvested at 9th day after germination (5 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581840" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581840/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23861838" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina, intermediate 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581840" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.i1, Petiole of the third leaf. Sample was collected at 9th day after germination (5 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581839" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581839/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25709347" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole, intermediate 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581839" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.y, Leaf blade of the third leaf. Sample was collected at 7th day after germination (3 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581838" foreground="98FF66" hex_colour="0x98ff66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581838/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29502586" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina of the young leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581838" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.y, Petiole of the third leaf. Sample was collected at 7th day after germination (3 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581837" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581837/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="35961155" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole of the young leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581837" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="R, Root without apex, collected from plants at 7th day after germination." record_number="SRR3581836" foreground="BD7740" hex_colour="0xbd7740" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581836/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25281241" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="root" svgname="ath-15dayOldSeedling.svg" description="Arabidopsis thaliana Root" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581836" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="R.A, Apex of the root, collected from plants at 7th day after germination." record_number="SRR3581835" foreground="8E826E" hex_colour="0x8e826e" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581835/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25255784" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-RootTip.svg" description="Arabidopsis thaliana Root Apex" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581835" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.R, Root of one-day old seedling. Immediately before collection seedlings were gently pulled out of soil and washed under fresh water." record_number="SRR3581834" foreground="C38C60" hex_colour="0xc38c60" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581834/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26221759" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="root" svgname="ath-youngSeedling.svg" description="Arabidopsis thaliana Seedling Root" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581834" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.C, Cotyledons of one-day-old seedling, collected with petioles." record_number="SRR3581833" foreground="99FF00" hex_colour="0x99ff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581833/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25468538" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="cotyledon" svgname="ath-youngSeedling.svg" description="Arabidopsis thaliana Seedling Cotyledons" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581833" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.M, Seedling shoot apical meristem with adjacent tissues." record_number="SRR3581831" foreground="979999" hex_colour="0x979999" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581831/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="56162722" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-ShootApexInflorescense.svg" description="Arabidopsis thaliana Seedling Meristem" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581831" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.H, Hypocotyl of one-day-old seedling from place of the attachment of cotyledons to the beginning of root." record_number="SRR3581740" foreground="CCCC98" hex_colour="0xcccc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581740/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25634721" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="hypocotyl" svgname="ath-youngSeedling.svg" description="Arabidopsis thaliana Seedling Hypocotyl" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581740" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="IN.sn, First elongated internode (from last rosette leaf to first cauline leaf). Sample was collected when first silique was yellow and ready to open." record_number="SRR3581738" foreground="0B539C" hex_colour="0x0b539c" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581738/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="31063954" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Internode.svg" description="Arabidopsis thaliana Senescent internode" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581738" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SL.sn2, Whole senescent silique 2. Sample was collected when first silique was yellow and ready to open." record_number="SRR3581737" foreground="937326" hex_colour="0x937326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581737/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27981806" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique1-5.svg" description="Arabidopsis thaliana Senescent silique 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581737" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="POD.sn1, Pod of the senescent silique 1. Sample was collected when first silique was yellow and ready to open." record_number="SRR3581736" foreground="929326" hex_colour="0x929326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581736/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24774839" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the senescent silique 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581736" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SD.sn1, Seeds from the senescent silique 1. Sample was collected when first silique was yellow and ready to open." record_number="SRR3581735" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581735/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="64890506" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Seeds from the senescent silique 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581735" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SD.g3, Seeds at third day after soaking." record_number="SRR3581734" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581734/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27717575" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-GerminatingSeed.svg" description="Arabidopsis thaliana Germinating seeds 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581734" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SD.g2, Seeds at second day after soaking." record_number="SRR3581733" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581733/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26673727" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-GerminatingSeed.svg" description="Arabidopsis thaliana Germinating seeds 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581733" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SD.g1, Seeds at first day after soaking." record_number="SRR3581732" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581732/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="37548470" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-GerminatingSeed.svg" description="Arabidopsis thaliana Germinating seeds 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581732" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SD.d, Dry seeds." record_number="SRR3581731" foreground="F77700" hex_colour="0xf77700" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581731/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27845864" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Dry Seeds" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581731" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="POD.y6-7, Pistils of 6th and 7th flowers (before pollination), ovules and stigma removed. Sample collected at the moment of the abscission of the first flower." record_number="SRR3581730" foreground="E7FF65" hex_colour="0xe7ff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581730/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="32902802" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="carpels" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Carpel of 6th and 7th flowers" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581730" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="STI, Stigmatic tissue from pistils of 6th and 7th flowers (before pollination). Sample collected at the moment of the abscission of the first flower." record_number="SRR3581728" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581728/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="32757267" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="Stigma_tissue" svgname="ath-StigmaAndOvaries.svg" description="Arabidopsis thaliana Stigmatic tissue" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581728" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="OV.y6-7, Ovules from 6th and 7th flowers (before pollination). Sample collected at the moment of the abscission of the first flower." record_number="SRR3581727" foreground="CCFF65" hex_colour="0xccff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581727/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27175344" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="Ovary_tissue" svgname="ath-StigmaAndOvaries.svg" description="Arabidopsis thaliana Ovules from 6th and 7th flowers" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581727" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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		<file info="SD.y5, Seeds from silique 5. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581726" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581726/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28691694" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed1-4.svg" description="Arabidopsis thaliana Young seeds 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581726" species="Arabidopsis thaliana">
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		<file info="SD.y4, Seeds from silique 4. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581724" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581724/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29368794" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Young seeds 4" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581724" species="Arabidopsis thaliana">
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		<file info="SD.y3, Seeds from silique 3. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581721" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581721/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="29325971" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Young seeds 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581721" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="SD.y2, Seeds from silique 2. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581720" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581720/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26162316" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Young seeds 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581720" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="SD.y1, Seeds from silique 1. All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581719" foreground="FFCC98" hex_colour="0xffcc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581719/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28045149" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Young seeds 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581719" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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			<groupwith>
				<bam_exp></bam_exp>
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		<file info="SL8, Whole silique 8. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581717" foreground="818211" hex_colour="0x818211" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581717/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="37024502" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique6-10.svg" description="Arabidopsis thaliana Silique 8" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581717" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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		<file info="POD7, Pod of the silique 7 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581716" foreground="B2B42A" hex_colour="0xb2b42a" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581716/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33847589" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 7" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581716" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="SD7, Seeds from silique 7. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581715" foreground="FECC00" hex_colour="0xfecc00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581715/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="41781463" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed1-4.svg" description="Arabidopsis thaliana Seeds 7" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581715" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
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				<bam_exp></bam_exp>
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		<file info="SL6, Whole silique 6. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581714" foreground="818211" hex_colour="0x818211" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581714/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33582097" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique6-10.svg" description="Arabidopsis thaliana Silique 6" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581714" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="POD5, Pod of the silique 5 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581713" foreground="B2B42A" hex_colour="0xb2b42a" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581713/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="32761627" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581713" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="SD5, Seeds from silique 5. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581712" foreground="FECC00" hex_colour="0xfecc00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581712/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="38727212" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Seeds 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581712" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="SL4, Whole silique 4. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581711" foreground="937326" hex_colour="0x937326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581711/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="34507004" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique1-5.svg" description="Arabidopsis thaliana Silique 4" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581711" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="POD3, Pod of the silique 3 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581710" foreground="929326" hex_colour="0x929326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581710/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="39198836" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581710" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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		<file info="SD3, Seeds from silique 3. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581709" foreground="FE9900" hex_colour="0xfe9900" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581709/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="35577557" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed5-7.svg" description="Arabidopsis thaliana Seeds 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581709" species="Arabidopsis thaliana">
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		<file info="SL2, Whole silique 2. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581708" foreground="937326" hex_colour="0x937326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581708/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="34861716" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Silique1-5.svg" description="Arabidopsis thaliana Silique 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581708" species="Arabidopsis thaliana">
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				<bam_exp></bam_exp>
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			</groupwith>
		</file>

		<file info="POD1, Pod of the silique 1 without seeds. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581707" foreground="929326" hex_colour="0x929326" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581707/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="35628361" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="silique" svgname="ath-WholeSilique.svg" description="Arabidopsis thaliana Pod of the silique 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581707" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="SD1, Seeds from silique 1. All samples of this series were taken at the moment when first silique is 1-1.5 cm long (corresponds to the moment of the abscission of the 8th flower). Before collection, siliques were washed in RNAlater solution in order to remove pollen." record_number="SRR3581706" foreground="FE9900" hex_colour="0xfe9900" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581706/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="39864995" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Seed8+.svg" description="Arabidopsis thaliana Seeds 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581706" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="IN, First elongated internode (from last rosette leaf to first cauline leaf). All samples are collected at the moment of the anthesis of the first flower." record_number="SRR3581705" foreground="99CCFF" hex_colour="0x99ccff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581705/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24803475" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-Internode.svg" description="Arabidopsis thaliana Internode" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581705" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="AX, Axis of the inflorescence without flowers and pedicels. All samples are collected at the moment of the anthesis of the first flower." record_number="SRR3581704" foreground="979999" hex_colour="0x979999" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581704/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24955209" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-ShootApexInflorescense.svg" description="Arabidopsis thaliana Axis of the inflorescence" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581704" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="PED, Pedicel of the first flower. All samples are collected at the moment of the anthesis of the first flower." record_number="SRR3581703" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581703/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24856659" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="receptacle" svgname="ath-Flower.svg" description="Arabidopsis thaliana Pedicel" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581703" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F19+, Whole inflorescence apex from flower 19 to meristem. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581702" foreground="FFFF66" hex_colour="0xffff66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581702/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26301511" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart19" svgname="ath-FlowerDevelopment19.svg" description="Arabidopsis thaliana Flowers 19 and following" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581702" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F15-18, Whole flowers 15, 16, 17 and 18 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581701" foreground="FFFF66" hex_colour="0xffff66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581701/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="34813777" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart15" svgname="ath-FlowerDevelopment15-18.svg" description="Arabidopsis thaliana Flowers 15-18" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581701" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F12-14, Whole flowers 12, 13 and 14 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581700" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581700/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27964107" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart12" svgname="ath-FlowerDevelopment12-14.svg" description="Arabidopsis thaliana Flowers 12-14" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581700" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F9-11, Whole flowers 9, 10 and 11 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581699" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581699/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28014618" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart9" svgname="ath-FlowerDevelopment9-11.svg" description="Arabidopsis thaliana Flowers 9-11" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581699" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F6-8, Whole flowers 6, 7 and 8 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581698" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581698/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25097184" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart6" svgname="ath-FlowerDevelopment6-8.svg" description="Arabidopsis thaliana Flowers 6-8" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581698" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F5, Whole flower 5 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581697" foreground="E8E846" hex_colour="0xe8e846" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581697/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24910430" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart5" svgname="ath-FlowerDevelopment5.svg" description="Arabidopsis thaliana Flower 5" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581697" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F4, Whole flower 4 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581696" foreground="D3D332" hex_colour="0xd3d332" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581696/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23475960" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart4" svgname="ath-FlowerDevelopment4.svg" description="Arabidopsis thaliana Flower 4" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581696" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F3, Whole flower 3 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581695" foreground="D3D332" hex_colour="0xd3d332" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581695/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26706614" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flowerDevelopmentPart3" svgname="ath-FlowerDevelopment3.svg" description="Arabidopsis thaliana Flower 3" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581695" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F2, Whole flower 2 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581694" foreground="CBCB32" hex_colour="0xcbcb32" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581694/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="22930187" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flower" svgname="ath-Flower.svg" description="Arabidopsis thaliana Flower 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581694" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F1, Whole flower 1 without pedicel. All samples of this series were collected at moment of the anthesis of the first flower." record_number="SRR3581693" foreground="CBCB32" hex_colour="0xcbcb32" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581693/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="28699725" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="flower" svgname="ath-Flower.svg" description="Arabidopsis thaliana Flower 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581693" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.SP.y, Sepals of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581692" foreground="CCFF65" hex_colour="0xccff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581692/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26634565" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="sepals" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Sepals of the young flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581692" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.AN.y, Anthers of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581691" foreground="FF5D5D" hex_colour="0xff5d5d" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581691/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="33172562" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="anthers" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Anthers of the young flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581691" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.CA.y, Pistil of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581690" foreground="CCFF65" hex_colour="0xccff65" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581690/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27107480" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="carpels" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Carpels of the young flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581690" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.SP.ad, Sepals of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581689" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581689/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24840129" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="sepals" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Sepals of the mature flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581689" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.PT.ad, Petals of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581688" foreground="CBCB32" hex_colour="0xcbcb32" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581688/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24299126" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petals" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Petals of the mature flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581688" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.FM.ad, Filaments of stamens of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581687" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581687/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="31363775" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="filament" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Stamen filaments of the mature flower" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581687" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.AN.ad, Anthers of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581686" foreground="FF5D5D" hex_colour="0xff5d5d" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581686/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23975035" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="anthers" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Anthers of the mature flower (before opening)" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581686" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.CA.ad, Pistil of the third flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581685" foreground="CAFF00" hex_colour="0xcaff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581685/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24976435" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="carpels" svgname="ath-FlowerParts.svg" description="Arabidopsis thaliana Carpels of the mature flower (before pollination)" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581685" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="F.AN, Anthers of first flower; sample collected at the moment of the anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581684" foreground="FF0000" hex_colour="0xff0000" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581684/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23673665" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="anthers" svgname="ath-Stamen.svg" description="Arabidopsis thaliana Opened Anthers" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581684" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.VN.sn, Midrib of the third leaf. Sample was collected when first silique was completely mature and nearly opened. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581683" foreground="0B539C" hex_colour="0x0b539c" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581683/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27631607" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="veins" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Vein of the senescent leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581683" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.sn, Petiole of the third leaf. Sample was collected when first silique was completely mature and nearly opened. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581682" foreground="0B539C" hex_colour="0x0b539c" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581682/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24944249" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole of the senescent leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581682" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.lg, Whole third leaf. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581681" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581681/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26437263" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="leaf" svgname="ath-leaf.svg" description="Arabidopsis thaliana Leaf, mature" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581681" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.lg, Parts of the leaf blade without veins. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581680" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581680/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27730456" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina of the mature leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581680" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.VN.lg, Midrib of the third leaf. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581679" foreground="007EFF" hex_colour="0x007eff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581679/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24330029" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="veins" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Vein of the mature leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581679" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.lg, Petiole of the third leaf. Sample was collected at the moment of anthesis of the first flower. All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581678" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581678/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="23104081" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole of the mature leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581678" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.i2, Parts of the leaf blade without veins. Sample was collected at 12th day after germination (10 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581676" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581676/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25790353" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina, intermediate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581676" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.VN.i2, Midrib of the third leaf. Sample was collected at 12th day after germination (10 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581672" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581672/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="27656275" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="veins" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Vein, intermediate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581672" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.i2, Petiole of third leaf. Sample was collected at 12th day after germination (10 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581639" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581639/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26728235" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole, intermediate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581639" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.i1, Leaf blade of the third leaf. Sample was harvested at 9th day after germination (5 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581591" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581591/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="34372243" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina, intermediate 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581591" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.i1, Petiole of the third leaf. Sample was collected at 9th day after germination (5 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581499" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581499/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25504210" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole, intermediate 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581499" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.LAM.y, Leaf blade of the third leaf. Sample was collected at 7th day after germination (3 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581388" foreground="98FF66" hex_colour="0x98ff66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581388/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24120483" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="lamina" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Lamina of the young leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581388" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="L.PET.y, Petiole of the third leaf. Sample was collected at 7th day after germination (3 mm leaf). All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf)." record_number="SRR3581383" foreground="00CBFF" hex_colour="0x00cbff" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581383/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="38460577" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="petiole" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Leaf Petiole of the young leaf" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581383" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="R, Root without apex, collected from plants at 7th day after germination." record_number="SRR3581356" foreground="BD7740" hex_colour="0xbd7740" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581356/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="26520999" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="root" svgname="ath-15dayOldSeedling.svg" description="Arabidopsis thaliana Root" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581356" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="R.A, Apex of the root, collected from plants at 7th day after germination." record_number="SRR3581352" foreground="8E826E" hex_colour="0x8e826e" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581352/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25732016" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-RootTip.svg" description="Arabidopsis thaliana Root Apex" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581352" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.R, Root of one-day old seedling. Immediately before collection seedlings were gently pulled out of soil and washed under fresh water." record_number="SRR3581347" foreground="C38C60" hex_colour="0xc38c60" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581347/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24534514" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="root" svgname="ath-youngSeedling.svg" description="Arabidopsis thaliana Seedling Root" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581347" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.C, Cotyledons of one-day-old seedling, collected with petioles." record_number="SRR3581345" foreground="0x99FF00" hex_colour="0x99ff00" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581345/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="25292910" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="cotyledon" svgname="ath-youngSeedling.svg" description="Arabidopsis thaliana Seedling Cotyledons" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581345" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.M, Seedling shoot apical meristem with adjacent tissues." record_number="SRR3581346" foreground="979999" hex_colour="0x979999" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581346/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="58953949" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-ShootApexInflorescense.svg" description="Arabidopsis thaliana Seedling Meristem" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581346" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="S.H, Hypocotyl of one-day-old seedling from place of the attachment of cotyledons to the beginning of root." record_number="SRR3581336" foreground="CCCC98" hex_colour="0xcccc98" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova/SRR3581336/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="24416101" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="hypocotyl" svgname="ath-youngSeedling.svg" description="Arabidopsis thaliana Seedling Hypocotyl" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3581336" species="Arabidopsis thaliana">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

				<file info="Third leaf was collected from 15 plants after cold treatment at 4C for 1 hour" record_number="SRR3724649" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova_Stress/SRR3724649/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="40986056" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Cold Treatment 1 hour Replicate 1" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3724649" species="Arabidopsis thaliana" title="Developmental transcriptome - Stress data - Klepikova et al/SRR3724649">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
			</groupwith>
		</file>

		<file info="Third leaf was collected from 15 plants after cold treatment at 4C for 1 hour" record_number="SRR3724650" foreground="65CC66" hex_colour="0x65cc66" bam_type="local" name="/DATA/eFP-Seq_Browser/bamdata_Developmental_transcriptome/Klepikova_Stress/SRR3724650/accepted_hits.bam" filename="accepted_hits.bam" total_reads_mapped="38739023" read_map_method="All RNA-seq reads were processed through a quality check and trimming pipeline using FastQC (Andrews, 2010)  and Trimmomatic (Bolger et al., 2014) respectively to remove residual adapters, low-quality sequences (the default criteria for Trimmomatic-0.32), and reads below 36 bp. Sequences from each library were aligned to the TAIR10 genome. Tophat version 2.1.1 with bowtie2 version 2.2.8 on UseGalaxy (Afgan et al., 2016) with the following custom parameters (rest remained default to UseGalaxy's settings): -i/--min-intron-length 50 -I/--max-intron-length 5000 . See Cheng, Krishnakumar et al. (2017) for more details. " publication_link="https://onlinelibrary.wiley.com/doi/10.1111/tpj.13312/abstract" svg_subunit="all" svgname="ath-LeafParts.svg" description="Arabidopsis thaliana Cold Treatment 1 hour Replicate 2" url="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3724650" species="Arabidopsis thaliana" title="Developmental transcriptome - Stress data - Klepikova et al/SRR3724650">
			<controls>
				<bam_exp></bam_exp>
			</controls>
			<groupwith>
				<bam_exp></bam_exp>
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		<!-- Until link has been fixed, this remain commented out
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		<!-- Until link has been fixed, this remain commented out
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