AIRR_minimal_standard
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1. STUDY, SUBJECT, DIAGNOSISComments
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Examples
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StudyPermanent identifier for each study
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Study titlePublication or protocol title
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Study typeEx. Placebo controlled phase 3 clinical trial
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Study Inclusion/Exclusion CriteriaStudy Inclusion/Exclusion Criteria; is this too detailed?
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Grant Funding AgencyEx. NIH
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Lab name
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Contact informationCorresponding author address, e-mail
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Contact information of person uploading data
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Lab address
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Relevant publication(s) give PMID or other identifierStudy associated publications
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SUBJECT
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Subject IDAn identifier for a person who is the subject in a study.
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Animal, human or syntheticDefine if it is a human, animal or synthetic based study
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SexSex of the subject
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AgeAge of the subject as number or description (eg, adult)
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Age EventEx. at enrollment, at T0, etc.
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Ancestry population
Immunogenomics Data analysis Working Group (IDAWG) and HLA-NET terms
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Ethnicityif permitted
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Raceif permitted
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Species NameTaxonomic group of organism
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Strain NameThe name of a strain of an organism variant
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Linked to other subjectother subject ID
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Type of linkFamily relationship, partner status, donor/acceptor
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DIAGNOSIS / INTERVENTION
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Examples
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Study Group DescriptionEx. Case vs. Control
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Diagnosis
Defined pathologic process with characteristic signs and symptoms
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Length of diseaseYears since diagnosis
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Disease stage
Position in the normal progression of the disease (ex. tumor, nodes, mets)
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Prior Therapies for the Primary Disease under studySurgery, medications etc.
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Immunogen/agentEx. Vaccine
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Intervention definitionDrug, Vaccine, Surgery etc.
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Other relevant medical historyPast medical history, medications, surgeries, other conditions
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2. SAMPLE and SAMPLE PROCESSING
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Examples
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Biological Sample IDID assigned to sample by investigator
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Sample typeTissue, body fluid
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Anatomic siteEx. spleen
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Disease state of sampleEx. tumor vs. margin
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Sample collection timeEx. day relative to event or time zero
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Collection Time Event (T0)Study Time T0 Event (eg, vaccination, recruitment, treatment)
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Source (from commercial)
If purchasing samples from a commercial source (company name)
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PROCESSING (cells)
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Examples
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Tissue Processing
Enzymatic digestion and/or physical methods used to isolate cells from sample
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Cell storageCryopreservation (Y/N)
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Cell qualityViability
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Cell qualityYield
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Cell isolation / enrichment procedureEx. flow cytometry or magnetic bead enrichment
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Cell stimulation or other procedureEx. overnight culture, stimulation with cytokines or cells etc.
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Cell subset
subset designation, list of markers used for flow sorting; fcs files for sort
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Single cell or bulk?
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How many cells in experiment?Number (if available)
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Number of cells per sequencing reactionNumber, if known
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Target substrateDNA or RNA
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DNA qualitymetric?
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RNA qualitymetric?
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Library generation methodEx. RACE or oligo (nested) amplification based
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Library generation protocolEnzymes, cycles, etc.
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Target Locus for PCRConstant region vs. V region amplification
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RNA: amplification of polyA or other (define) to generate cDNA
specify the the technology for RT reaction
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Description of how barcodes and primers are organized
short description about the general set-up of the amplicon generation, cellular and sample barcode layout (if applicable); description must include a mapping between samples and barcodes
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Unique molecular identifier (UMI or UID)describe set-up of molecular identifiers, if they are used
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Forward PCR Primer Target LocationEx. FR1, etc.
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Reverse PCR Primer Target LocationEx. Constant region, etc.
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Forward PCR Primer SequencesSequence of the Forward PCR Primer Sequences
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Reverse PCR Primer SequencesSequence of the Reverse PCR Primer Sequences
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whole vs. partial sequencesIs the entire V(D)J region sequenced? (Y/N)
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Heavy vs. light chain vs. paired
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ng of template (for bulk sequencing)ng of template used for primary amplification (e.g. RNA or DNA)
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Total reads passing QC filter(s)
Number of usable reads for analysis; comes directly off of the sequencer
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Calibrator and other internal controlsDefine PhiX, calibrators, internal controls, if used
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Protocol ID(s)Protocol IDs from the sequencing run
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Sequencing Platform
sequencing instrument and software version and any changes that have been made to the software
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Read length(s)
Specified as (Read 1 length, Read 2 length) or the average depending on the instrument
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Sequencing Facility
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Ex. Company, Core Facility, Lab Name
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Batch number
Recorded batch number or ID; mapping of samples to batches, lanes, specific flow cells
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Date of sequencing run (to identify problematic runs)
Date when the sequencing runs were processed
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Sequencing kitManufacturer, Catalog Number, Lot number
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4. FASTQ file containing the raw sequences
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5. PROCESSING (software)
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Examples
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version numbers for software toolsversion number and / or date, include company pipelines
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paired read assembly
How paired end reads were assembled into a single receptor sequence
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quality thresholds
How sequences were removed from (4) based on base quality scores
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primer match cutoffs
How primers were identified in the sequences, were they removed/masked/etc?
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collapsing method
The method used for combining multiple sequences from (4) into a single sequence in (5)
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data processing protocols (free text)General description of how QC is performed
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6. FASTA or FASTQ file containing the processed sequences
The final processed antigen receptor sequences used for V(D)J assignment
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