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add new assay template spatial transcriptomics #187

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Merged
MasterPastures merged 4 commits into from
Jul 14, 2025
Merged

add new assay template spatial transcriptomics #187

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98bce50
add new assay template spatial transcriptomics
ameliakallaher Jul 14, 2025
e0f5e98
Merge 98bce50f13f6389ddd08759440f61c78912a24b1 into 49913e718db1ad237…
ameliakallaher Jul 14, 2025
5282d28
GitHub Action: assemble *.model.csv from modules directory
ameliakallaher Jul 14, 2025
7e92c94
GitHub Action: convert *.model.csv to *.model.jsonld
ameliakallaher Jul 14, 2025
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1 change: 1 addition & 0 deletions AD.model.csv
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Expand Up @@ -1057,6 +1057,7 @@ assay_rnaArray_metadata_template,SysBio rnaArray metadata template schema,,"Comp
assay_rnaSeq_metadata_template,SysBio rnaSeq metadata template schema,,"Component, specimenID, libraryID, assay, platform, RIN, referenceSet, rnaBatch, libraryBatch, sequencingBatch, libraryPrep, libraryPreparationMethod, libraryVersion, isStranded, readStrandOrigin, readLength, runType, totalReads, validBarcodeReads, DV200, inputTotalRNA, ribosomalDepletion,globinRemoval",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.rnaSeq,,,template
assay_scrnaSeq_metadata_template,SysBio scrnaSeq metadata template schema,,"Component, specimenID, libraryID, assay, platform, sampleBarcode, RIN, referenceSet, rnaBatch, libraryBatch, sequencingBatch, libraryPrep, libraryPreparationMethod, libraryVersion, libraryType, isStranded, readStrandOrigin, readLength, runType, totalReads, validBarcodeReads, numberCells, medianGenes, medianUMIs",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.scrnaSeq,,,template
assay_snpArray_metadata_template,SysBio snpArray metadata template schema,,"Component, specimenID, assay, platform, dnaBatch, arrayBatch, ratio260over280, ratio260over230, GQN",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.snpArray,,,template
assay_spatialTranscriptomics_metadata_template,SysBio spatial transcriptomics metadata template schema,,"Component, individualID, biospecimenID, fileFormat, sequenceAnalysis, runID, captureArea, readIndicator, spatialRead1, spatialRead2, spatialLibraryConstructionMethod, samplePreparation, libraryPreparationDaysFromIndex, sequencingLibraryConstructionDaysFromIndex, endBias, reverseTranscriptionPrimer, sequencingPlatform, protocolLink, slideVersion, slideID, imageReorientation, permeabilizationOnTime, RIN, DV200, CDNALength, CDNAOffset, spatialBarcodeOffset, spatialBarcodeLength, UMIBarcodeOffset, UMIBarcodeLength, featureReferenceID, checkSum, UMITag, whitelistSpatialBarcodeFileLink, spatialBarcodeTag, appliedHardTrimming, alignedReadLength, workflowVersion, workflowLink, spotsUnderTissue, meanReadsPerSpatialSpot, medianNumberGenesPerSpatialSpot, sequencingSaturation, proportionReadsMapped, readsMappedToTranscriptome, medianUMICountsPerSpot",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.spatialTranscriptomics,,,template
assay_STARRSeq_metadata_template,SysBio STARRSeq metadata template schema,,"Component, specimenID, libraryID, assay, platform, RIN, dnaBatch, referenceSet, rnaBatch, libraryBatch, sequencingBatch, libraryPrep, libraryPreparationMethod, libraryVersion, isStranded, readStrandOrigin, readLength, runType, totalReads, validBarcodeReads, numberCells, medianGenes, medianUMIs, ratio260over280, ratio260over230, GQN",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.STARRSeq,,,template
assay_TMTquantitation_metadata_template,SysBio TMTquantitation (aka proteomics) metadata template schema,,"Component, specimenID, assay, platform, controlType, batch, batchChannel, TMTType, fragmentation, resolution, multiconsensusStudyFileID",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.TMTquantitation,,,template
assay_wholeExomeSeq_metadata_template,SysBio wholeExomeSeq metadata template schema,,"Component, specimenID, libraryID, assay, platform, referenceSet, dnaBatch, sequencingBatch, libraryPrep, libraryPreparationMethod, readLength, runType, totalReads, ratio260over280, ratio260over230, GQN",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.wholeExomeSeq,,,template
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