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assay whole genome sequencing template

Template for Whole_Genome_Sequencing [Download]

Attribute Description Required columnType DependsOn Source Parent Valid Values
libraryBatchID Library batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
measurementTechnique The name of the measurement technique describing the assay method. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
readLengthUnits The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified True STRING ManifestColumn
referenceTranscriptID The ID for the transcript/gene. Either the NCBI ID or the Ensembl ID must be provided. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
repositoryName The public repository name for the transcript (for example, Ensembl or NCBI Gene) True STRING ManifestColumn ArrayExpress,Broad Single Cell Portal,dbGAP,ENA,Ensembl,FlowRepository,GenBank,GENCODEv38 GRCh38, GEO,GISAID,IEDB,ImmPort,MassIVE,MetaboLights,Metabolomics Workbench,MGnify,NCBI Gene,PRIDE,SRA,UniProt
resultUnit The unit for the result value True STRING ManifestColumn FPKM,raw count, Not applicable,Not collected,Not specified,RPKM,TPM,Unknown
rnaBatchID Isolation batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
sampleType The type of sample collected or the term used to describe the source of a biospecimen used for a laboratory test. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
sequencingBatchID Sequencing batch identifier, provided by the data contributor to Sage Bionetworks. The batch identifier(s) must be stored in a data dictionary .csv file uploaded to Synapse. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
technologyPlatformVersion The specific version (application, manufacturer, model, lab, etc.) of a technology that is used to carry out a laboratory or computational experiment. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING ManifestColumn
transcriptType The type of transcript reported True STRING ManifestColumn lincRNA,mRNA,total RNA minus rRNA,Not applicable,Not collected,Not specified,Other,snRNA,Unknown
valueReported The count or gene count for the transcript True NUMBER ManifestColumn
Component False
Filename False
specimenID Identifying string linked to a particular sample or specimen, provide by the data contributor True STRING sage.annotations-experimentalData.specimenID-0.0.2 ManifestColumn
platformLocation The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING sage.annotations-experimentalData.platformLocation-0.0.2 ManifestColumn
isStranded Whether or not the library is stranded. True BOOLEAN sage.annotations-ngs.isStranded-0.0.2 ManifestColumn FALSE,TRUE
libraryPrep The general strategy by which the library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING sage.annotations-ngs.libraryPrep-0.0.13 ManifestColumn amplicon, cellHashing, Chromium Single Cell 3', DNALibraryConstruction, EndItDNAEndRepairKit, KapaHyperPrep, lncRNAenrichment, methylSeq, miRNAenrichment, multiome, MULTIseq, PCRfree, polyAselection, proximity ligation, rRNAdepletion, snIsoSeq, SPLITseq, STARRSeq, SureCell, totalRNA, Unknown, Not collected, Not applicable, Not specified
libraryPreparationMethod Method by which library was prepared. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING sage.annotations-ngs.libraryPreparationMethod-0.0.10 ManifestColumn 10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit, Qiagen PreAnalytiX PAXgene Blood miRNA Kit, Unknown, Not collected, Not applicable, Not specified
libraryVersion Library Version- for example, rnaSeq 10x library version. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified True STRING sage.annotations-ngs.libraryVersion-0.0.2 ManifestColumn
readLength The length of the read. Provide a value or Unknown Not collected Not applicable Not specified True STRING sage.annotations-ngs.readLength-0.0.2 ManifestColumn
readStrandOrigin The strand from which the read originates in a strand-specific protocol. True STRING sage.annotations-ngs.readStrandOrigin-0.0.2 ManifestColumn forward, reverse, stranded, unstranded, Unknown, Not collected, Not specified, Not applicable
runType The type of run True STRING sage.annotations-ngs.runType-0.0.2 ManifestColumn Not applicable,Not collected,Not specified,pairedEnd,singleEnd,singleEnd pairedEnd,Unknown
totalReads Total number of sequencing reads from a library. True STRING sage.annotations-experimentalData.totalReads-0.0.2 ManifestColumn