Analyte

Summary of SMaHT Portal object type Analyte . Types referencing this type are: AlignedReads, File, HistologyImage, Library, OutputFile, ReferenceFile, SubmittedFile, SupplementaryFile, UnalignedReads, VariantCalls. Property names in red are required properties; those in blue are identifying properties; and properties with types in green are reference properties.


Description: Analyte items contain information on molecules extracted from samples for subsequent analysis.

Tip

See actual Analyte data here

Required Properties

Property Type Description
molecule array of enum See below for more details.
molecule_detail array of enum See below for more details.
samples Sample
array of string 		See below for more details.
submission_centers SubmissionCenter
array of string 		See below for more details.
See values here
submitted_id string See below for more details.

Identifying Properties

Property Type Description
accession string See below for more details.
submitted_id string See below for more details.
uuid string See below for more details.

Reference Properties

Property Type Description
analyte_preparation AnalytePreparation
string 		See below for more details.
consortia Consortium
array of string 		See below for more details.
See values here
protocols Protocol
array of string 		See below for more details.
samples Sample
array of string 		See below for more details.
submission_centers SubmissionCenter
array of string 		See below for more details.
See values here

Properties

Property Type Description
a260_a280_ratio number
• min value: 0
 Ratio of nucleic acid absorbance at 260 nm and 280 nm, used to determine a measure of DNA purity.
accession string A unique identifier to be used to reference the object. [Only admins are allowed to set or update this value.]
alternate_accessions array of string
• restricted
 Accessions previously assigned to objects that have been merged with this object. [Only admins are allowed to set or update this value.]
analyte_preparation AnalytePreparation
• string
 Link to associated analyte preparation.
average_fragment_size number
• min value: 0
 Average high molecular weight fragment size, if applicable (bp).
concentration number
• min value: 0
 Analyte concentration.
concentration_unit
 • mg/mL
 • ng/uL 		enum of string Unit of the concentration.
consortia Consortium
• array of string
• unique
 Consortia associated with this item.
See values here
description string Plain text description of the item.
display_title string
• calculated
 -
dna_integrity_number number
• min value: 1
• max value: 10
 Assessment of the integrity of genomic DNA based on electrophoresis.
dna_integrity_number_instrument string Instrument used for DIN assessment.
dna_quality_number number
• min value: 0
• max value: 10
 DNA Quality Number, percent of samples above threshold value.
dna_quality_number_instrument string Instrument used for DNA quality number assessment.
dna_quality_size_threshold number
• min value: 0
 Threshold set in ProSize for DNA quality number, for assessing percent of samples above threshold size (bp), if applicable.
external_id string External ID for the item provided by submitter.
Must adhere to (regex) pattern: ^[A-Za-z0-9-_]{3,}$
genomic_quality_number number
• min value: 0
• max value: 10
 Genomic quality number, percent of samples above threshold value.
genomic_quality_number_instrument array of string Instrument used for GQN assessment.
genomic_quality_size_threshold number
• min value: 0
 Threshold set in ProSize for genomic quality number, for assessing percent of samples above threshold size (bp), if applicable.
molecule
 • DNA
 • RNA 		array of enum
• min items: 1
• unique
 Molecule of interest for the analyte.
molecule_detail
 • MicroRNA
 • Total DNA
 • Total RNA
 • mRNA
 • rRNA
 • tRNA 		array of enum
• min items: 1
• unique
 Biological features included in the analyte.
protocols Protocol
• array of string
• min items: 1
• unique
• restricted
 Protocols providing experimental details.
quantitation_method array of string
• min items: 1
• unique
 Method used for analyte quantitation, if applicable.
ribosomal_rna_ratio number
• min value: 0
 The 28S/18S ribosomal RNA band ratio used to assess the quality of total RNA.
rna_integrity_number number
• min value: 1
• max value: 10
 Assessment of the integrity of RNA based on electrophoresis (or equivalent RNA Quality Score or RNA Quality Number).
rna_integrity_number_instrument string Instrument used for RNA integrity assessment.
sample_quantity number
• min value: 0
 The amount of sample used to generate the analyte.
sample_quantity_unit
 • cells
 • g
 • mL
 • mg
 • ng
 • uL
 • ug 		enum of string Unit of the sample quantity.
samples Sample
• array of string
• min items: 1
• max items: 1000
• unique
 Link to associated samples (e.g. Tissue Sample, Cell Culture Sample, etc.).
status
 • deleted
 • draft
 • in review ← default
 • obsolete
 • public
 • released
 • restricted 		enum of string
• default: in review
 -
submission_centers SubmissionCenter
• array of string
• unique
 Submission Centers that created this item.
See values here
submitted_id string Unique identifier for the item assigned by the submitter.
Must adhere to (regex) pattern: ^[A-Z0-9]{3,}_ANALYTE_[A-Z0-9-_.]{4,}$
tags array of string
• min string length: 1
• max string length: 50
• unique
• restricted
 Key words that can tag an item - useful for filtering.
Must adhere to (regex) pattern: ^[a-zA-Z0-9|_-]+$
total_yield number
• min value: 0
 Total yield of analyte from sample (ug).
uuid string Unique ID by which this object is identified.
volume number
• min value: 0
 Analyte volume.
volume_unit
 • mL
 • uL 		enum of string Unit of the volume.
yield_per_unit number
• min value: 0
 Yield per unit of sample.
yield_unit
 • ug/mg
 • ug/million cells
 • ug/vial of cells 		enum of string Unit used for measuring yield per unit of sample.