Merge pull request #175 from adknowledgeportal/clear-ad_rnaseq_updates

updated rnaSeq template

Author: MasterPastures

AD.model.csv

@@ -919,6 +919,7 @@ geneticBackground,This refers to the population's specific line of ancestral des
 geneticMutations,These are strain-level genetic mutations. This should follow the format gene-allele. Example: Trem2-R47H,,,,False,ManifestColumn,,sage.annotations-neuro.geneticMutations-0.0.1,,string,MODEL-AD 
 genotype,Genotype common name,,,,True,ManifestColumn,,sage.annotations-clinical.genotype-0.0.2,,string,mouse
 genotypeBackground,Genetic background of the model,,,,True,ManifestColumn,,sage.annotations-clinical.genotypeBackground-0.0.2,,string,mouse
+globinRemoval,"true,false",,,,False,ManifestColumn,,sage.annotations-experimentalData.globinRemoval-0.0.2,,string,sequencing
 GQN,Illumina Genomic Quality Number (gDNA quality score),,,,False,ManifestColumn,,sage.annotations-qc.GQN-0.0.3,,number,sequencing
 grant,"Grant number including activity code, institute code, and serial number (e.g. U01MH103392)",,,,True,ManifestColumn,,sage.annotations-neuro.grant-0.0.2,,string,ADKP
 height,For CLEAR AD. UDSV3 IVP Form B1 Physical Question 1 Numeric XX.X (inches). Use 888 for not assessed.,,,,False,ManifestColumn,,sage.annotations-demographics.height-0.0.2,,string,demographics
@@ -929,6 +930,7 @@ hypertension,For CLEAR-AD. UDSV3 IVP Form A5 Subject Health History Question 5b.
 individualID,Identifying string linked to the individual or animal being studied,,,,False,ManifestColumn,,sage.annotations-experimentalData.individualID-0.0.2,required^^#FileAnnotationTemplate,string,individual
 individualIdSource,Database or repository to which individual ID maps,"ABN, ABR, ADNI, AIBS, BannerSun, BEB_Miller, Caltech, Clotomics_PAIKEA_MSSM, DongLab, Einstein, Emory, Geschwind, HBSFRC, HBTRC, JAX, LIBD, LivingBrainProject_MSSM, MayoBrainBank, Mayo Clinic, MSSM, NDRI, Newcastle, NICHD, NIMH-HBCC, Novogenix, NYBB, Oxford, Penn, PGP, Pitt, Pritzker, Rush, Sestan, SMRI, StemExpress, TAA, UCI_TMF, UCSF, UM-BTB, UW-CDL, Vaccarino, XCell Science, Yale, IU, Mayo Clinic, University of Miami, University of Florida, Washington University, Michigan University, NACC",,,False,ManifestColumn,,sage.annotations-experimentalData.individualIdSource-0.0.17,required^^#IndividualHumanMetadataTemplate,string,individual
 INFA,Infarcts and lacunes. Reports of anoxic ischemic injury will not be considered within the infarcts and lacunes lesions,"No, Yes, missing or unknown",,,False,ManifestColumn,,sage-annotations-clinical.INFA-0.0.2,string,,clinical
+inputTotalRNA,In nanogram before rRNA depletion and globin removal,,,,False,ManifestColumn,,sage.annotations-experimentalData.inputTotalRNA-0.0.11,,string,sequencing
 INT,Interval between last exam and death (unit in months). Use missing or unknown if not available,,,,True,ManifestColumn,,sage-annotations-clinical.INT-0.0.2,string,,clinical
 ionMode,"Ionization polarity (positive, negative, polar)",,,,False,ManifestColumn,,sage.annotations-experimentalData.ionMode-0.0.2,,string,mass spectrometry
 isModelSystem,,"TRUE, FALSE",,,True,ManifestColumn,,sage.annotations-neuro.isModelSystem-0.0.2,,boolean,ADKP
@@ -942,7 +944,7 @@ LEWY_grp,Kosaka LBD subtypes grouped and PD Braak grouped,"No LEWY_grp or olfact
 libraryBatch,Batch library was prepared in,,,,False,ManifestColumn,,sage.annotations-batch.libraryBatch-0.0.2,,string,batch
 libraryID,Library ID as provided by the lab,,,,False,ManifestColumn,,sage.annotations-ngs.libraryID-0.0.2,,string,sequencing
 libraryPrep,The general strategy by which the library was prepared,"amplicon, cellHashing, Chromium Single Cell 3', DNALibraryConstruction, EndItDNAEndRepairKit, KapaHyperPrep, lncRNAenrichment, methylSeq, miRNAenrichment, multiome, MULTIseq, PCRfree, polyAselection, proximity ligation, rRNAdepletion, snIsoSeq, SPLITseq, STARRSeq, SureCell, totalRNA",,,True,ManifestColumn,,sage.annotations-ngs.libraryPrep-0.0.13,,string,sequencing
-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
+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
 libraryType,"The type of library, in assays where samples are barcoded or hashed for multiplexing or each sample has multiple libraries amplified separately before pooled sequencing.","ADT, cDNA, CMO, HTO, LMO, plasmid DNA",,,False,ManifestColumn,,sage.annotations-ngs.libraryType-0.0.3,,string,sequencing
 libraryVersion,"Library Version: for example, rnaSeq 10x library version",,,,False,ManifestColumn,,sage.annotations-ngs.libraryVersion-0.0.2,,string,sequencing
 ligand,"An ion, molecule or molecular group that binds to a substance to form a larger complex.",,,,False,ManifestColumn,,sage.annotations-experimentalData.ligand-0.0.2,,string,experimentalData
@@ -976,7 +978,7 @@ organ,A unique macroscopic (gross) anatomic structure that performs specific fun
 passage,Number of times a cell culture has been subcultured,,,,False,ManifestColumn,,sage.annotations-experimentalData.passage-0.0.2,,integer,biospecimen
 pcrCycles,Number of PCR cycles to amplify transposased DNA fragments,,,,False,ManifestColumn,,sage.annotations-experimentalData.pcrCycles-0.0.2,,integer,sequencing
 pH,A scale used to specify the acidity or basicity of an aqueous or other liquid solution. pH for intracellular tissue in the brain,,,,False,ManifestColumn,,sage.annotations-neuro.pH-0.0.3,,string,clinical
-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
+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
 platformLocation,Laboratory where data generation platform was located,,,,False,ManifestColumn,,sage.annotations-experimentalData.platformLocation-0.0.2,,string,experimentalData
 PMI,Post-mortem interval (unit in hours). Use missing or unknown if not available,,,,False,ManifestColumn,,sage.annotations-neuro.PMI-0.0.3,#NeuropathMetadataTemplate required^^,string,clinical
 pmiUnits,Time units used to record the post-mortem interval,"hours, minutes",,,False,ManifestColumn,,sage.annotations-neuro.PMI-0.0.3,#NeuropathMetadataTemplate required^^,string,clinical
@@ -991,6 +993,7 @@ registryAbbreviation,Specify the registry. Example: JR_004807,,,,False,ManifestC
 reprogrammingMethod,The method by which source cells were reprogrammed into pluripotent stem cells.,"CytoTune iPS 2.0 Sendai Reprogramming Kit, episomal vectors, Sendai virus",,,False,ManifestColumn,,sage.annotations-experimentalData.reprogrammingMethod-0.0.2,,string,biospecimen
 resolution,Minimum nominal mass-over-charge (m/z) difference detectable,,,,False,ManifestColumn,,sage.annotations-experimentalData.resolution-0.0.2,,number,mass spectrometry
 resourceType,The type of resource being stored and annotated,"analysis, curatedData, experimentalData, metadata, report, tool",,,True,ManifestColumn,,sage.annotations-sageCommunity.resourceType-0.0.5,,string,ADKP
+ribosomalDepletion,"true,false",,,,False,ManifestColumn,,sage.annotations-experimentalData.ribosomalDepletion-0.0.2,,string,sequencing
 RIN,RNA Integrity Number,,,,False,ManifestColumn,,sage.annotations-qc.RIN-0.0.2,,number,sequencing
 rnaBatch,Batch in which RNA sample was isolated,,,,False,ManifestColumn,,sage.annotations-batch.rnaBatch-0.0.2,,string,batch
 rodentDiet,Laboratory rodent diet,"4% standard, 6% standard, 7% standard, 45% high-fat diet, 5W80 western diet",,,True,ManifestColumn,,sage.annotations-neuro.rodentDiet-0.0.1,,string,mouse
@@ -1051,7 +1054,7 @@ assay_MRI_metadata_template,SysBio MRI metadata template schema,,"Component, ind
 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
 assay_PET_metadata_template,SysBio PET metadata template schema,,"Component, individualID, scanID, ligand, platform, ageAssessment, ageAssessmentUnits",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.PET,,,template
 assay_rnaArray_metadata_template,SysBio rnaArray metadata template schema,,"Component, specimenID, assay, RIN, platform, rnaBatch, arrayBatch",,False,ManifestTemplate,,sysbio.metadataTemplates-assay.rnaArray,,,template
-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
+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_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