assay bsSeq template
Template for bsSeq [Source]
| Attribute | Description | Required | columnType | DependsOn | Source | Parent | Valid Values |
|---|---|---|---|---|---|---|---|
| conversionRatio | The ratio or % detailing how well the bisulfite conversion worked. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | ManifestColumn | |||
| conversionRatioUnits | The units of measurement. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | ManifestColumn | |||
| dnaBatchID | DNA 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 | |||
| dnaBatchSize | The number of samples. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | ManifestColumn | |||
| dnaBatchSizeUnit | The unit of measurement for number of samples in a batch | True | STRING | ManifestColumn | AFU,AI,AU/ml,bp g/dl,DK units/ml,g/l,gm,HAU,IU,iu/l,IU/ml,Kallikrein Inactivator Unit per Milliliter,kg,l,M,mg,mg/dl,mg/l,mg/ml,miu/ml,ml,mM,MOI,ng,ng/dl,ng/ml,ng/nl,ng/ul,nl,nM,Not specified,NPX,optical density,other,PFU,PFUe,pg,pg/mg creatinine,pg/ml,pg/nl,pg/ul,pl,pM,Pound,TCID50,ug,ug/dl,ug/l,ug/ml,ug/ul,uiu/ml,ul,uM,umol/l,units/ml,Unknown,Not collected,Not applicable,Not specified | ||
| enrichmentMethod | The method used for performing an enrichment of specific regions by a restriction enzyme digest. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified | True | STRING | ManifestColumn | |||
| 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 | |||
| 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 | |||
| sequencingBatchSize | The number of samples. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | ManifestColumn | |||
| sequencingBatchSizeUnit | The unit of measurement for number of samples in a batch. Provide a value or 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 | |||
| 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 | ||
| directionalBSseqLibrary | Indicates whether or not the bisulfiteSeq library is directional | True | STRING | sage.annotations-ngs.directionalBSseqLibrary-0.0.2 | ManifestColumn | TRUE, FALSE, Unknown, Not collected, Not applicable, Not specified | |
| gDNAconc | gDNA Concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | sage.annotations-experimentalData.gDNAconc-0.0.3 | ManifestColumn | ||
| isStranded | Whether or not the library is stranded. | True | BOOLEAN | sage.annotations-ngs.isStranded-0.0.2 | ManifestColumn | FALSE,TRUE | |
| lambdaDNAconc | Lambda DNA spike-in concentration in ng. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | sage.annotations-experimentalData.lambdaDNAconc-0.0.2 | ManifestColumn | ||
| 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 | ||
| meanCoverage | Total number of bases covered by ATAC-seq reads/size of genome. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | sage.annotations-qc.meanCoverage-0.0.2 | ManifestColumn | ||
| pcrCycles | Number of PCR cycles to amplify transposased DNA fragments. Provide a value or Unknown Not collected Not applicable Not specified | True | STRING | sage.annotations-experimentalData.pcrCycles-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 |