assay whole genome sequencing template
Template for Whole_Genome_Sequencing [Source]
| 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,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,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,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, 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, 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 |