reagent.md

Reagent

Model definitions

FluorescentStain

Description of a fluorescent stain

Field	Type	Title (Description)
probe	GeneProbe or ProteinProbe or SmallMoleculeProbe	Target of the stain
stain_type	StainType	Stain type
fluorophore	Fluorophore	Fluorophore used in the stain
initiator_name	Optional[str]	Initiator for HCR probes
name	str	Name
source	Organization	Source
rrid	Optional[PIDName]	Research Resource ID
lot_number	Optional[str]	Lot number
expiration_date	Optional[datetime.date]	Lot expiration date

Fluorophore

Flurophore used in HCR, Immunolabeling, etc

Field	Type	Title (Description)
fluorophore_type	FluorophoreType	Fluorophore type
excitation_wavelength	int	Excitation wavelength (nm)
excitation_wavelength_unit	SizeUnit	Excitation wavelength unit

GeneProbe

Description of a set of oligonucleotide probes targeting a specific gene

Field	Type	Title (Description)
gene	PIDName	Gene name
probes	Optional[List[OligoProbe]]	Probes

GeneProbeSet

set of probes used in BarSEQ

Field	Type	Title (Description)
gene_probes	List[GeneProbe]	Gene probes
name	str	Name
source	Organization	Source
rrid	Optional[PIDName]	Research Resource ID
lot_number	Optional[str]	Lot number
expiration_date	Optional[datetime.date]	Lot expiration date

OligoProbe

Description of an oligonucleotide probe

Field	Type	Title (Description)
name	str	Name
sequence	str	Sequence

ProbeReagent

Description of a probe used as a reagent

Field	Type	Title (Description)
target	GeneProbe or ProteinProbe or SmallMoleculeProbe	Target
name	str	Name
source	Organization	Source
rrid	Optional[PIDName]	Research Resource ID
lot_number	Optional[str]	Lot number
expiration_date	Optional[datetime.date]	Lot expiration date

ProteinProbe

Description of a protein probe including antibodies

Field	Type	Title (Description)
protein	PIDName	Target protein name
species	Optional[Species]	Species of the probe
mass	float	Mass of protein probe (ug)
mass_unit	MassUnit	Mass unit
sequence	Optional[str]	Amino acid sequence of the probe

Reagent

Description of reagent used in procedure

Field	Type	Title (Description)
name	str	Name
source	Organization	Source
rrid	Optional[PIDName]	Research Resource ID
lot_number	Optional[str]	Lot number
expiration_date	Optional[datetime.date]	Lot expiration date

SmallMoleculeProbe

Description of a small molecule probe

Field	Type	Title (Description)
molecule	PIDName	Target small molecule name
mass	float	Mass of small molecule probe (ug)
mass_unit	MassUnit	Mass unit

Solution

Description of a solution made in house. Should match a solution named in protocol.

Field	Type	Title (Description)
name	str	Name
lot_number	Optional[str]	Lot number