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ameliakallaherameliakallaher
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updated rnaSeq template
1 parent 4201920 commit 5abc798

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‎modules/experimentalData/platform.csv‎

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Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
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platform,"The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment.","Affy5.0, Affy6.0, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133AB, AffymetrixU133Plus2, Agilent44Karray, BGISEQ-500, Biocrates p180, Biograph mCT, Bionano Irys, Bruker Avance III, confocalImaging, ddSEQ Single-Cell Isolator, DNBSEQ, GAIIx, HiSeq1000, HiSeq2000, HiSeq2500, HiSeq3000, HiSeq4000, HiSeqX, Illumina_1M, Illumina_h650, Illumina_HumanOmni1-Quadv1.0, llumina Infinium General Screening Array 24-Kit v3.0, Illumina MouseWG-6 v2.0 expression beadchip, Illumina_Omni2.5-8, Illumina_Omni2.5-8_v1.1, Illumina_Omni2.5-8_v1.3, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina_Omni5-Quad, IlluminaHumanHap300, IlluminaHumanHap650Yv3_A, IlluminaHumanHT-12_V3_0_R1, IlluminaHumanMethylation450, IlluminaMethylationEPIC, IlluminaInfiniumGSAMD-24v2-0, Illumina_Infinium-HumanMethylation450-BeadChip, IlluminaMiSeq, Illumina NovaSeq 6000, IlluminaNovaseq6000, IlluminaWholeGenomeDASL, Infinium Global Diversity Array-8, Infinium HumanOmniExpressExome, Infinium Omni2.5Exome-8 v1.1, Infinium Omni2.5Exome-8 v1.3, Infinium Omni2.5Exome-8 v1.4, Infinium Omni2.5Exome-8 v1.5, InfiniumPsychArrayBeadChip, Leco Pegasus IV, LTQOrbitrapXL, MiSeq, NanostringnCounter, NanostringnCounter_MouseADPanel, NextSeq500, NextSeq2000, Olink Target 96, orbitrap, Orbitrap Exploris 240, OrbiTrap Fusion, Orbitrap Fusion Lumos, PacBioRSII, PacBio Sequel II, PacBio Sequel IIe, Perlegen300Karray, PsychChip, Q Exactive, Q Exactive HF, Q Exactive HF-X, Q Exactive Plus, quadrupole time-of-flight, Roche Cobas, SequenomMultiplex, Signa Premier AIR 3T, Simoa HD-1 Analyzer, time-of-flight, triple quadrupole, Xevo G2 QTOF, Xevo TQ-S",,,True,ManifestColumn,,sage.annotations-experimentalData.platform-0.0.26,,string,experimentalData
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platform,"The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment.","Affy5.0, Affy6.0, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133AB, AffymetrixU133Plus2, Agilent44Karray, BGISEQ-500, Biocrates p180, Biograph mCT, Bionano Irys, Bruker Avance III, confocalImaging, ddSEQ Single-Cell Isolator, DNBSEQ, GAIIx, HiSeq1000, HiSeq2000, HiSeq2500, HiSeq3000, HiSeq4000, HiSeqX, Illumina_1M, Illumina_h650, Illumina_HumanOmni1-Quadv1.0, llumina Infinium General Screening Array 24-Kit v3.0, Illumina MouseWG-6 v2.0 expression beadchip, Illumina_Omni2.5-8, Illumina_Omni2.5-8_v1.1, Illumina_Omni2.5-8_v1.3, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina_Omni5-Quad, IlluminaHumanHap300, IlluminaHumanHap650Yv3_A, IlluminaHumanHT-12_V3_0_R1, IlluminaHumanMethylation450, IlluminaMethylationEPIC, IlluminaInfiniumGSAMD-24v2-0, Illumina_Infinium-HumanMethylation450-BeadChip, IlluminaMiSeq, Illumina NovaSeq 6000, IlluminaNovaseq6000,IlluminaNovaSeqXplus,IlluminaNovaSeqX, IlluminaWholeGenomeDASL, Infinium Global Diversity Array-8, Infinium HumanOmniExpressExome, Infinium Omni2.5Exome-8 v1.1, Infinium Omni2.5Exome-8 v1.3, Infinium Omni2.5Exome-8 v1.4, Infinium Omni2.5Exome-8 v1.5, InfiniumPsychArrayBeadChip, Leco Pegasus IV, LTQOrbitrapXL, MiSeq, NanostringnCounter, NanostringnCounter_MouseADPanel, NextSeq500, NextSeq2000, Olink Target 96, orbitrap, Orbitrap Exploris 240, OrbiTrap Fusion, Orbitrap Fusion Lumos, PacBioRSII, PacBio Sequel II, PacBio Sequel IIe, Perlegen300Karray, PsychChip, Q Exactive, Q Exactive HF, Q Exactive HF-X, Q Exactive Plus, quadrupole time-of-flight, Roche Cobas, SequenomMultiplex, Signa Premier AIR 3T, Simoa HD-1 Analyzer, time-of-flight, triple quadrupole, Xevo G2 QTOF, Xevo TQ-S",,,True,ManifestColumn,,sage.annotations-experimentalData.platform-0.0.26,,string,experimentalData
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Affy5.0,Affymetrix Genome-Wide Human SNP 5.0 Array,,,,,platform,,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6804,,string,experimentalData
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Affy6.0,Affymetrix Genome-Wide Human SNP 6.0 Array,,,,,platform,,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6801,,string,experimentalData
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Affymetrix Human Gene 1.0 ST Array,Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] in situ oligonucleotide,,,,,platform,,https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6244,,string,experimentalData

‎modules/sequencing/globinRemoval.csv‎

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Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
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globinRemoval,"true,false",,,,False,ManifestColumn,,sage.annotations-experimentalData.globinRemoval-0.0.2,,string,sequencing

‎modules/sequencing/inputTotalRNA.csv‎

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Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
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inputTotalRNA,In nanogram before rRNA depletion and globin removal,,,,False,ManifestColumn,,sage.annotations-experimentalData.inputTotalRNA-0.0.11,,string,sequencing

‎modules/sequencing/libraryPreparationMethod.csv‎

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Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
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libraryPreparationMethod,Method by which library was prepared,"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",,,False,ManifestColumn,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,,string,sequencing
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libraryPreparationMethod,Method by which library was prepared,"10x, Accel-NGS 2S Plus, Accel-NGS Methyl-Seq, CEL-seq, Drop-Seq,Illumina Ligation, NEBNext, NexteraXT, Omni-ATAC, sac-seq, Smart-seq1, Smart-seq2, Smart-seq4, SMRTbell, TruSeq, Ultralow Methyl-Seq, Illumina DNA PCR-Free Prep Kit,Enzymatics (Qiagen)",,,False,ManifestColumn,,sage.annotations-ngs.libraryPreparationMethod-0.0.10,,string,sequencing
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10x,10x Genomics library preparation,,,,,libraryPreparationMethod,,https://github.com/HumanCellAtlas/metadata-schema/blob/master/json_schema/type/process/sequencing/library_preparation_process.json,,string,sequencing
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Accel-NGS 2S Plus,"The Accel-NGS 2S Plus DNA Library Kit, designed for Illumina platforms, utilizes a proprietary adapter attachment chemistry which minimizes bias and supports inputs as low as 10 pg.",,,,,libraryPreparationMethod,,https://swiftbiosci.com/accel-ngs-2s-plus-dna-library-kit/,,string,sequencing
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Accel-NGS Methyl-Seq,Accel-NS Methyl-Seq technology utilizes Illumina-compatible adapter sequences and has been validated for whole genome bisulfite sequencing (WGBS) and targeted sequencing through hybridization capture.,,,,,libraryPreparationMethod,,https://www.bioscience.co.uk/userfiles/pdf/PRT-019%20Methyl-Seq%20Protocol%20Rev%203%20(1).pdf,,string,sequencing

‎modules/sequencing/ribosomalDepletion.csv‎

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Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules,columnType,module
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ribosomalDepletion,"true,false",,,,False,ManifestColumn,,sage.annotations-experimentalData.ribosomalDepletion-0.0.2,,string,sequencing

‎modules/template/templates.csv‎

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assay_nanostring_metadata_template,SysBio nanostring metadata template schema,,"Component, specimenID, assay, platform, RIN, rnaBatch, libraryBatch, nanostringBatch, libraryPrep, libraryPreparationMethod, geneRLF, bindingDensity",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.nanostring,,,template
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assay_PET_metadata_template,SysBio PET metadata template schema,,"Component, individualID, scanID, ligand, platform, ageAssessment, ageAssessmentUnits",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.PET,,,template
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assay_rnaArray_metadata_template,SysBio rnaArray metadata template schema,,"Component, specimenID, assay, RIN, platform, rnaBatch, arrayBatch",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.rnaArray,,,template
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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",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.rnaSeq,,,template
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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
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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
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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
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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

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