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HTAN.model.csv

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1073 lines (1073 loc) · 370 KB
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AttributeDescriptionValid ValuesDependsOnPropertiesRequiredParentDependsOn ComponentSourceValidation Rules
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AssayA planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.[OBI_0000070]FALSEhttp://purl.obolibrary.org/obo/OBI_0000070
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DeviceA thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipmentFALSEAssayhttps://w3id.org/biolink/vocab/Device
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SequencingModule for next generation sequencing assaysFALSEAssay
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ComponentCategory of metadata (e.g. Diagnosis, Biospecimen, scRNA-seq Level 1, etc.); provide the same one for all items/rows.TRUEhttps://w3id.org/biolink/vocab/category
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PatientHTAN patientComponent, HTAN Participant IDFALSEIndividual OrganismDemographics, Family History, Exposure, Follow Up, Diagnosis, Therapy, Molecular Test
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FileA type of Information Content Entity specific to OSFALSEInformation Content Entityhttps://w3id.org/biolink/vocab/DataFile
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FilenameName of a fileTRUEregex search ^.+\/\S*$
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File FormatFormat of a file (e.g. txt, csv, fastq, bam, etc.)hdf5, bedgraph, idx, idat, bam, bai, excel, powerpoint, tif, tiff, OME-TIFF, png, doc, pdf, fasta, fastq, sam, vcf, bcf, maf, bed, chp, cel, sif, tsv, csv, txt, plink, bigwig, wiggle, gct, bgzip, zip, seg, html, mov, hyperlink, svs, md, flagstat, gtf, raw, msf, rmd, bed narrowPeak, bed broadPeak, bed gappedPeak, avi, pzfx, fig, xml, tar, R script, abf, bpm, dat, jpg, locs, Sentrix descriptor file, Python script, sav, gzip, sdf, RData, hic, ab1, 7z, gff3, json, sqlite, svg, sra, recal, tranches, mtx, tagAlign, dup, DICOM, czi, mex, cloupe, am, cell am, mpg, m, mzML,scn, dcc, rcc, pkc, sf, bedpeTRUE
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CDS Sequencing TemplateCDS compatible template file, includes attributes for Genomic Reference, Library Layout, Data Type, Sequencing Platform, Library Selection MethodComponent, Filename, File Format, HTAN Data File ID, HTAN Parent Biospecimen ID, CDS library_id, CDS library_strategy, CDS library_source, CDS library_selection, CDS library_layout, CDS platform, CDS instrument_model, CDS design_description, CDS reference_genome_assembly, CDS custom_assembly_fasta_file_for_alignment, CDS bases, CDS number_of_reads, CDS coverage, CDS avg_read_length, CDS sequence_alignment_softwareTRUE
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CDS library_idShort unique identifier for the sequencing library.TRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS library_strategyLibrary strategyAMPLICON, ATAC-seq, Bisulfite-Seq, ChIA-PET, ChIP-Seq, CLONE, CLONEEND, CTS, DNase-Hypersensitivity, EST, FAIRE-seq, FINISHING, FL-cDNA, Hi-C, MBD-Seq, MeDIP-Seq, miRNA-Seq, MNase-Seq, MRE-Seq, ncRNA-Seq, OTHER, POOLCLONE, RAD-Seq, RIP-Seq, RNA-Seq, SELEX, ssRNA-seq, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, Tn-Seq, WCS, WGA, WGS, WXSTRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS library_sourceThe Library Source specifies the type of source material that is being sequencedGENOMIC, GENOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, OTHER, SYNTHETIC, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, VIRAL RNATRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS library_selectionLibrary Selection Method5-methylcytidine antibody, CAGE, cDNA, cDNA_oligo_dT, cDNA_randomPriming, CF-H, CF-M, CF-S, CF-T, ChIP, DNAse, HMPR, Hybrid Selection, Inverse rRNA, MBD2 protein methyl-CpG binding domain, MDA, MF, MNase, MSLL, Oligo-dT, other, Padlock probes capture method, PCR, PolyA, RACE, RANDOM, RANDOM PCR, Reduced Representation, repeat fractionation, Restriction Digest, RT-PCR, size fractionation, unspecifiedTRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS library_layoutPaired-end or SinglePaired-end, Single-endTRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS platformSequencing Platform used for SequencingLS454, ABI_SOLID, BGISEQ, CAPILLARY, COMPLETE_GENOMICS, HELICOS, ILLUMINA, ION_TORRENT, OXFORD_NANOPORE, PACBIO_SMRTTRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS instrument_modelInstrument model used for sequencing454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX+, 454 GS FLX Titanium, 454 GS Junior, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina iSeq 100, Illumina NovaSeq 6000, Illumina MiniSeq, Illumina MiSeq, NextSeq 500, NextSeq 550, Helicos HeliScope, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500x-Wl Genetic Analyzer, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, Complete Genomics, PacBio RS, PacBio RS II, PacBio Sequel, PacBio Sequel II, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5 XL, Ion Torrent S5, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, GridION, MinION, PromethION, BGISEQ-500, DNBSEQ-G400, DNBSEQ-T7, DNBSEQ-G50, MGISEQ-2000RSTRUESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS design_descriptionFree-form description of the methods used to create the sequencing library; a brief 'materials and methods' section.FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS reference_genome_assemblyThis is only if you are submitting a bam file aligned against a NCBI assembly.FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS custom_assembly_fasta_file_for_alignmentPlease provide the name of the custom assembly fasta file used during alignmentFALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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CDS basesCount of unique basecalls present in the data. Please count each base only once if using secondary alignments.FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesint
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CDS number_of_readsCount of the number of reads in the data. Please count each read only once if using secondary alignments.FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesint
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CDS coverageDepth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length)FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesint
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CDS avg_read_lengthFound by (Bases)/(Reads)FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesint
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CDS sequence_alignment_softwareThe name of the software program used to align nucleotide sequencing data.FALSESequencinghttps://dataservice.datacommons.cancer.gov/#/resourcesstr
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ChecksumMD5 checksum of the BAM fileTRUEInformation Content Entity
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HTAN Data File IDSelf-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz)TRUEFilehttps://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharingregex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
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HTAN Participant IDHTAN ID associated with a patient based on HTAN ID SOP (eg HTANx_yyy )TRUEPatienthttps://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharingregex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))$ warning
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HTAN Biospecimen IDHTAN ID associated with a biosample based on HTAN ID SOP (eg HTANx_yyy_zzz)TRUEBiospecimenhttps://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharingregex match ^(HTA([1-9]|1[0-6]))_((EXT)?([0-9]\d*|0000))_([0-9]\d*|0000)$ warning
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HTAN Parent IDHTAN ID of parent from which the biospecimen was obtained. Parent could be another biospecimen or a research participant.TRUEBiospecimenhttps://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing
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HTAN Parent Biospecimen IDHTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separatedTRUEBiospecimenhttps://docs.google.com/document/d/1podtPP8L1UNvVxx9_c_szlDcU1f8n7bige6XA_GoRVM/edit?usp=sharing
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HTAN Parent Data File IDHTAN Data File Identifier indicating the file(s) from which these files were derivedTRUEFile
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Clinical Data Tier 2Tier 2 Cancer DataComponent, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Sentinel Lymph Node Count, Sentinel Node Positive Assessment Count, Tumor Extranodal Extension Indicator, Satellite Metastasis Present Indicator, Other Biopsy Resection Site, Extent of Tumor Resection, Prior Sites of Radiation, Immunosuppression, Concomitant Medication Received Type, Family Member Vital Status Indicator, COVID19 Occurrence Indicator, COVID19 Current Status, COVID19 Positive Lab Test Indicator, COVID19 Antibody Testing, COVID19 Complications Severity, COVID19 Cancer Treatment Followup, Ecig vape use, Ecig vape 30 day use num, Ecig vape times per day, Type of smoke exposure cumulative years, Chewing tobacco daily use count, Second hand smoke exposure years, Known Genetic Predisposition Mutation, Hereditary Cancer Predisposition Syndrome, Cancer Associated Gene Mutations, Mutational Signatures, Mismatch Repair System Status, Lab Tests for MMR Status, Mode of Cancer Detection, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence LocationFALSEPatient
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SRRS Clinical Data Tier 2Cancer related clinical data specific to SRRSComponent, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Education Level, Country of Birth, Medically Underserved Area, Rural vs Urban, Cancer Incidence, Cancer Incidence Location, Ethnicity, Gender, Race, Vital Status, Age at Diagnosis, Days to Last Follow up, Days to Last Known Disease Status, Days to Recurrence, Last Known Disease Status, Morphology, Primary Diagnosis, Progression or Recurrence, Site of Resection or Biopsy, Tissue or Organ of Origin, NCI Atlas Cancer Site, Tumor Grade, Pack Years Smoked, Years Smoked, Days to Follow Up, Gene Symbol, Molecular Analysis Method, Test Result, Treatment Type, Tumor Largest Dimension DiameterFALSEPatient
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Lung Cancer Tier 3Lung cancer specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Lung Cancer Detection Method Type, Lung Cancer Participant Procedure History, Lung Adjacent Histology Type, Lung Tumor Location Anatomic Site, Lung Tumor Lobe Bronchial Location, Current Lung Cancer Symptoms, Lung Topography, Lung Cancer Harboring Genomic AberrationsFALSEPatient
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Colorectal Cancer Tier 3Colorectal cancer specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Colorectal Cancer Detection Method Type, History of Prior Colon Polyps, Family Colon Cancer History Indicator, Family Medical History Colorectal Polyp Diagnosis, Immediate Family History Endometrial Cancer, Immediate Family History Ovarian Cancer, Patient Inflammatory Bowel Disease Personal Medica History, Patient Colonoscopy Performed Indicator, Colorectal Cancer Tumor Border Configuration, MLH1 Promoter Methylation Status, Colorectal Cancer KRAS Indicator, Colon Polyp Occurence Indicator, Family History Colorectal Polyp, Colorectal Polyp New Indicator, Colorectal Polyp Shape, Size of Polyp Removed, Colorectal Polyp Count, Colorectal Polyp Type, Colorectal Polyp Adenoma TypeFALSEPatient
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Breast Cancer Tier 3Breast cancer specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Breast Carcinoma Detection Method Type, Breast Carcinoma Histology Category, Invasive Lobular Breast Carcinoma Histologic Category, Invasive Ductal Breast Carcinoma Histologic Category, Breast Biopsy Procedure Finding Type, Breast Quadrant Site, Breast Cancer Assessment Tests, Breast Cancer Genomic Test Performed, Mammaprint Risk Group, Oncotype Risk Group, Breast Carcinoma Estrogen Receptor Status, Breast Carcinoma Progesteroner Receptor Status, Breast Cancer Allred Estrogen Receptor Score, Prior Invasive Breast Disease, Breast Carcinoma ER Status Percentage Value, Breast Carcinoma PR Status Percentage Value, HER2 Breast Carcinoma Copy Number Total, Breast Carcinoma Centromere 17 Copy Number, Breast Carcinoma HER2 Centromere17 Copynumber Total, Breast Carcinoma HER2 Chromosome17 Ratio, Breast Carcinoma Surgical Procedure Name, Breast Carcinoma HER2 Ratio Diagnosis, Breast Carcinoma HER2 Status, Hormone Therapy Breast Cancer Prevention Indicator, Breast Carcinoma ER Staining Intensity, Breast Carcinoma PR Staining Intensity, Oncotype Score, Breast Imaging Performed Type, Multifocal Breast Carcinoma Present Indicator, Multicentric Breast Carcinoma Present Indicator, BIRADS Mammography Breast Density CategoryFALSEPatient
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Neuroblastoma and Glioma Tier 3Brain cancer specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,CNS Tumor Primary Anatomic Site, Glioma Specific Metastasis Sites, Glioma Specific Radiation Field, Supra Tentorial Ependymoma Molecular Subgroup, Infra Tentorial Ependymoma Molecular Subgroup, Neuroblastoma MYCN Gene Amplification StatusFALSEPatient
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Acute Lymphoblastic Leukemia Tier 3Acute Lymphoblastic Leukemia attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Specimen Blast Count Percentage Value, NCI ALL Risk Group, MRD ALL Diagnostic Sensitivity, CNS Leukemia StatusFALSEPatient
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Ovarian Cancer Tier 3Ovarian cancer specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Ovarian Cancer Histologic Subtype, Ovarian Cancer Surgical Outcome, Ovarian Cancer Platinum StatusFALSEPatient
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Prostate Cancer Tier 3Prostate cancer specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Location Extent Extraprostatic Extension, Location Nature Positive Margins, Seminal Vesicle Invasion, Prostate Carcinoma Histologic Type, Prostate Cancer Local Extent, Additonal Findings Uninvolved Prostate, Prostate Cancer Cytologic Morphologic SubtypesFALSEPatient
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Sarcoma Tier 3Sarcoma specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Sarcoma Subtype, Sarcoma Diagnosis Classification Category, Sarcoma Tumor Extension TypeFALSEPatient
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Pancreatic Cancer Tier 3Pancreatic cancer specific attributes in Clinical Tier Data 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index,Pancreas Precancer Histopathologic Grade, Pancreatic IPMN Pathology Epithelial Subtype, Pancreatic Duct Final Pathology TypeFALSEPatient
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Melanoma Tier 3Melanoma specific attributes in Clinical Data Tier 3Component, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Cutaneous Melanoma Tumor Infiltrating Lymphocytes, Cutaneous Melanoma Tumor Regression Range, Melanoma Specimen Clark Level Value, Cutaneous Melanoma Surgical Margins, Melanoma Lesion Size, History of Atypical Nevi, Fitzpatrick Skin Tone, History of Chronic UV Exposure, History of Blistering Sunburn, History of Tanning Bed Use, Immediate Family History Melanoma, Melanoma Biopsy Resection Sites, Cutaneous Melanoma Ulceration, Cutaneous Melanoma Additional FindingsFALSEPatient
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DemographicsDemographic attributesComponent, HTAN Participant ID, Ethnicity, Gender, Race, Vital Status, Days to Birth, Country of Residence, Age Is Obfuscated, Year Of Birth, Occupation Duration Years, Premature At Birth, Weeks Gestation at BirthFALSEPatient
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Family HistoryFamily cancer historyComponent, HTAN Participant ID, Relative with Cancer HistoryFALSEPatient
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ExposureExposure to carcinogensComponent, HTAN Participant ID, Start Days from Index, Smoking Exposure, Alcohol Exposure, Asbestos Exposure, Coal Dust Exposure, Environmental Tobacco Smoke Exposure, Radon Exposure, Respirable Crystalline Silica ExposureFALSEPatient
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Follow UpFollow up clinical visitsComponent, HTAN Participant ID, Days to Follow Up, Adverse Event, Progression or Recurrence, Barretts Esophagus Goblet Cells Present, BMI, Cause of Response, Comorbidity, Comorbidity Method of Diagnosis, Days to Adverse Event, Days to Comorbidity, Diabetes Treatment Type, Disease Response, DLCO Ref Predictive Percent, ECOG Performance Status, FEV1 FVC Post Bronch Percent, FEV 1 FVC Pre Bronch Percent, FEV1 Ref Post Bronch Percent, FEV1 Ref Pre Bronch Percent, Height, Hepatitis Sustained Virological Response, HPV Positive Type, Karnofsky Performance Status, Menopause Status, Pancreatitis Onset Year, Reflux Treatment Type, Risk Factor, Risk Factor Treatment, Viral Hepatitis Serologies, Weight, Adverse Event Grade, AIDS Risk Factors, Body Surface Area, CD4 Count, CDC HIV Risk Factors, Days to Imaging, Evidence of Recurrence Type, HAART Treatment Indicator, HIV Viral Load, Hormonal Contraceptive Use, Hysterectomy Margins Involved, Hysterectomy Type, Imaging Result, Imaging Type, Immunosuppressive Treatment Type, Nadir CD4 Count, Pregnancy Outcome, Recist Targeted Regions Number, Recist Targeted Regions Sum, Scan Tracer UsedFALSEPatient
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TherapyClinical therapy or treatmentComponent, HTAN Participant ID, Treatment or Therapy, Treatment Type, Treatment Effect, Treatment Outcome, Days to Treatment End, Treatment Anatomic Site, Days to Treatment Start, Initial Disease Status, Regimen or Line of Therapy, Therapeutic Agents, Treatment Intent Type, Chemo Concurrent to Radiation, Number of Cycles, Reason Treatment Ended, Treatment Arm, Treatment Dose, Treatment Dose Units, Treatment Effect Indicator, Treatment FrequencyFALSEPatient
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DiagnosisDisease diagnosisComponent, HTAN Participant ID, Age at Diagnosis, Year of Diagnosis, Primary Diagnosis, Precancerous Condition Type, Site of Resection or Biopsy, Tissue or Organ of Origin, Morphology, Tumor Grade, Progression or Recurrence, Last Known Disease Status, Days to Last Follow up, Days to Last Known Disease Status, Method of Diagnosis, Prior Malignancy, Prior Treatment, Metastasis at Diagnosis, Metastasis at Diagnosis Site, First Symptom Prior to Diagnosis, Days to Diagnosis, Percent Tumor Invasion, Residual Disease, Synchronous Malignancy, Tumor Confined to Organ of Origin, Tumor Focality, Tumor Largest Dimension Diameter, Gross Tumor Weight, Breslow Thickness, Vascular Invasion Present, Vascular Invasion Type, Anaplasia Present, Anaplasia Present Type, Laterality, Perineural Invasion Present, Lymphatic Invasion Present, Lymph Nodes Positive, Lymph Nodes Tested, Peritoneal Fluid Cytological Status, Classification of Tumor, Best Overall Response, Mitotic Count, AJCC Clinical M, AJCC Clinical N, AJCC Clinical Stage, AJCC Clinical T, AJCC Pathologic M, AJCC Pathologic N, AJCC Pathologic Stage, AJCC Pathologic T, AJCC Staging System Edition, Cog Neuroblastoma Risk Group, Cog Rhabdomyosarcoma Risk Group, Gleason Grade Group, Gleason Grade Tertiary, Gleason Patterns Percent, Greatest Tumor Dimension, IGCCCG Stage, INPC Grade, INPC Histologic Group, INRG Stage, INSS Stage, International Prognostic Index, IRS Group, IRS Stage, ISS Stage, Lymph Node Involved Site, Margin Distance, Margins Involved Site, Medulloblastoma Molecular Classification, Micropapillary Features, Mitosis Karyorrhexis Index, Non Nodal Regional Disease, Non Nodal Tumor Deposits, Ovarian Specimen Status, Ovarian Surface Involvement, Pregnant at Diagnosis, Primary Gleason Grade, Secondary Gleason Grade, Supratentorial Localization, Tumor Depth, WHO CNS Grade, WHO NTE GradeFALSEPatient
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Molecular TestClinical molecular test dataComponent, HTAN Participant ID, Timepoint Label, Start Days from Index, Stop Days from Index, Gene Symbol, Molecular Analysis Method, Test Result, AA Change, Antigen, Clinical Biospecimen Type, Blood Test Normal Range Upper, Blood Test Normal Range Lower, Cell Count, Chromosome, Clonality, Copy Number, Cytoband, Exon, Histone Family, Histone Variant, Intron, Laboratory Test, Loci Abnormal Count, Loci Count, Locus, Mismatch Repair Mutation, Molecular Consequence, Pathogenicity, Ploidy, Second Exon, Second Gene Symbol, Specialized Molecular Test, Test Analyte Type, Test Units, Test Value, Transcript, Variant Origin, Variant Type, ZygosityFALSEPatient
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BiospecimenHTAN biological entity; this can be tissue, blood, analyte and subsamples of thoseComponent, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Timepoint Label, Collection Days from Index, Adjacent Biospecimen IDs, Biospecimen Type, Acquisition Method Type, Fixative Type, Storage Method, Processing Days from Index, Protocol Link, Site Data Source, Collection Media, Mounting Medium, Processing Location, Histology Assessment By, Histology Assessment Medium, Preinvasive Morphology, Tumor Infiltrating Lymphocytes, Degree of Dysplasia, Dysplasia Fraction, Number Proliferating Cells, Percent Eosinophil Infiltration, Percent Granulocyte Infiltration, Percent Inflam Infiltration, Percent Lymphocyte Infiltration, Percent Monocyte Infiltration, Percent Necrosis, Percent Neutrophil Infiltration, Percent Normal Cells, Percent Stromal Cells, Percent Tumor Cells, Percent Tumor Nuclei, Fiducial Marker, Slicing Method, Lysis Buffer, Method of Nucleic Acid IsolationFALSEBiosamplePatient
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SRRS BiospecimenSRRS-specific HTAN biological entity; this can be tissue, blood, analyte and subsamples of those, however it can be described via fewer attributes than a standard HTAN specimenComponent, HTAN Biospecimen ID, Source HTAN Biospecimen ID, HTAN Parent ID, Adjacent Biospecimen IDs, Biospecimen Type, Timepoint Label, Collection Days from Index, Acquisition Method Type, Ischemic Time, Ischemic Temperature, Collection Media, Topography Code, Additional Topography, Fixative Type, Storage Method, Preinvasive Morphology, Histologic Morphology Code, Preservation Method, Processing Days from Index, Protocol LinkFALSEBiosamplePatient
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Source HTAN Biospecimen IDThis is the HTAN ID that may have been assigned to the biospecimen at the site of biospecimen origin (e.g. BU).FALSEBiosample
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Other AssayMetadata applying to any assay without standard descriptors. Can be used as a placeholder for minimal amount of metadata until the assay descriptors are standardizedComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay TypeFALSEAssayBiospecimen
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ExSeq MinimalMinimal metadata for the ExSeq assayComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Assay TypeFALSEAssayBiospecimen
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Assay TypeThe type and level of assay this metadata applies to (e.g. RPPA, NanoString DSP, etc.)TRUEAssay
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scRNA-seq Level 1Single-cell RNA-seq [EFO_0008913]Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method, Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate GroupFALSESequencingBiospecimenhttp://www.ebi.ac.uk/efo/EFO_0008913
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scRNA-seq Level 2Alignment workflows downstream of scRNA-seq Level 1Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard TrimmingFALSESequencingscRNA-seq Level 1
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scRNA-seq Level 3Gene and Isoform expression filesComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow VersionFALSESequencingscRNA-seq Level 2
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scRNA-seq Level 4Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow LinkFALSESequencingscRNA-seq Level 3
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Slide-seq Level 1Raw sequencing files for the Slide-seq assay.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Read Indicator, Spatial Read1, Spatial Read2, End Bias, Reverse Transcription Primer, Spatial Barcode Offset, Spatial Barcode and UMI, Spike In, Sequencing Platform, Technical Replicate Group, Protocol Link, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from IndexFALSESpatial TranscriptomicsBiospecimen
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Slide-seq Level 2Aligned sequencing files and QC for the Slide-seq assay.Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Spatial Barcode Tag, Matched Spatial Barcode Tag, UMI Tag, Applied Hard TrimmingFALSESpatial TranscriptomicsSlide-seq Level 1
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Slide-seq Level 3Gene matrices with features and barcodes for Slide-seq as well as spatial information (bead location files).Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Sequencing Batch ID, Data Category, Matrix Type, Slide-seq Workflow Type, Workflow Version, Slide-seq Workflow Parameter Description, Workflow Link, Beads Total, Median UMI Counts per Spot, Median Number Genes per Spatial Spot, Slide-seq Bead File Type, Slide-seq Fragment SizeFALSESpatial TranscriptomicsSlide-seq Level 2
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Slide-seq Fragment SizeAverage cDNA length associated with the experiemtn. IntegerFALSESpatial Transcriptomics
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Matched Spatial Barcode TagSAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific)TRUESpatial Transcriptomics
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Beads TotalNumber of sequenced beads. Applies to raw counts matrix only. IntegerFALSESpatial Transcriptomics
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Slide-seq Workflow TypeGeneric name for the workflow used to analyze the Slide-seq data set. StringTRUESpatial Transcriptomics
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Slide-seq Workflow Parameter DescriptionParameters used to run the Slide-seq workflow. StringTRUESpatial Transcriptomics
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Slide-seq Bead File TypeThe type of Level 3 file submitted as part of the Slide-seq workflow.Matrix Features, Matrix Barcodes, All Bead Locations, All Bead Barcodes, Matched Bead Barcodes, Matched Bead Locations, Not ApplicableTRUESpatial Transcriptomics
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Bulk RNA-seq Level 1Bulk RNA-seq [EFO_0003738]Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Library Layout, Read Indicator, Nucleic Acid Source, Micro-region Seq Platform, ROI Tag, Sequencing Platform, Sequencing Batch ID, Read Length, Library Selection Method, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Library Preparation Days from Index, Spike In, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Transcript Integrity Number, RIN, DV200, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow LinkFALSESequencingBiospecimenhttp://www.ebi.ac.uk/efo/EFO_0003738
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Bulk RNA-seq Level 2Bulk RNA-seq alignment protocol descriptionComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Is lowest levelFALSESequencingBulk RNA-seq Level 1
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Bulk RNA-seq Level 3Bulk RNA-seq gene expression matricesComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Pseudo Alignment Used, Data Category, Expression Units, Matrix Type, Fusion Gene Detected, Fusion Gene IdentityFALSESequencingBulk RNA-seq Level 2
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Bulk WES Level 1Bulk Whole Exome Sequencing raw filesComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Read Indicator, Library Selection Method, Read Length, Target Capture Kit, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Sequencing Platform, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Multiplex Barcode, Library Preparation Days from Index, Size Selection Range, Target Depth, To Trim Adapter SequenceFALSESequencingBiospecimen
75
Bulk WES Level 2Bulk Whole Exome Sequencing aligned files and QCComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Adapter Content, Basic Statistics, Encoding, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, QC Workflow Type, QC Workflow Version, QC Workflow Link, MSI Workflow Link, MSI Score, MSI Status, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X,Is lowest levelFALSESequencingBulk WES Level 1
76
Bulk WES Level 3Bulk Whole Exome Sequencing called variantsComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Genomic Reference, Genomic Reference URL, Germline Variants Workflow URL, Germline Variants Workflow Type, Somatic Variants Workflow URL, Somatic Variants Workflow Type, Somatic Variants Sample Type, Structural Variant Workflow URL, Structural Variant Workflow TypeFALSESequencingBulk WES Level 2
77
Microarray Level 1Microarray Level 1 refers to the raw text table of probe level intensitiesComponent, Filename, File Format, HTAN Data File ID, HTAN Participant ID, HTAN Parent Biospecimen ID, Nucleic Acid Source, Microarray Platform ID, Microarray Molecule, Microarray Label, Microarray Value Definition, Microarray Protocol Auxiliary FileFALSEAssayBiospecimen
78
Microarray Level 2Microarray Level 2 provides a normalized matrix of values.Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Microarray Platform ID, Normalization MethodFALSEAssayMicroarray Level 1
79
scATAC-seq Level 1scATAC-seq files containing sequence read information, with or without alignment, as FASTQ or BAM filesComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Dissociation Method, Single Nucleus Buffer, Single Cell Isolation Method, Transposition Reaction, scATACseq Library Layout, Nucleus Identifier, Nuclei Barcode Length, Nuclei Barcode Read, scATACseq Read1, scATACseq Read2, scATACseq Read3, Library Construction Method, Sequencing Platform, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Median Fraction of Reads in Peaks, Median Fraction of Reads in Annotated cis DNA Elements, Median Passing Read Percentage, Median Percentage of Mitochondrial Reads per Nucleus,Technical Replicate Group, Total Reads, Protocol LinkFALSESequencingBiospecimen
80
scATAC-seq Level 2scATAC-seq files containing aligned sequence data, as a BAM fileComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Median Percentage of Mitochondrial Reads per Nucleus, Contamination,Contamination ErrorFALSESequencingscATAC-seq Level 1
81
scATAC-seq Level 3Processed data files containing peak information for cellsComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATAC-seq Object ID, nCount Peaks, nFeature Peaks, Total Read-Pairs, Duplicate Read-Pairs, Chimeric Read-Pairs, Unmapped Read-Pairs, LowMapQ, Mitochondrial Read-Pairs, Passed Filters, TSS Fragments, DNase Sensitive Region Fragments, Enhancer Region Fragments, Promoter Region Fragments, On Target Fragments, Blacklist Region Fragments, Peak Region Fragments, Peak Region Cutsites, Nucleosome Signal, Nucleosome Percentile, TSS Enrichment, TSS Percentile, Pct Reads in Peaks, Blacklist Ratio, Seurat Clusters, nCount RNA, nFeature RNA, MACS2 Seqnames, MACS2 Start, MACS2 End, MACS2 Width, MACS2 Strand, MACS2 Name, MACS2 Score, MACS2 Fold Change, MACS2 Neg Log10 pvalue Summit, MACS2 Neg Log10 qvalue Summit, MACS2 Relative Summit PositionFALSESequencingscATAC-seq Level 2
82
scmC-seq Level 1Files contain raw scmC-seq data.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, scmCseq Read1, scmCseq Read2, scmCseq Read3, Single Cell Isolation Method, Single Nucleus Buffer, Single Nucleus Capture, Bisulfite Conversion, Library Layout, Nucleus Identifier, Sequencing Platform, Technical Replicate Group, Median Fraction of Reads in Peaks, Median Passing Read Percentage, Peaks Calling Software, Median Percentage of Mitochondrial Reads per Nucleus, Threshold for Minimum Passing Reads, Total Number of Passing Nuclei, Total ReadsFALSESequencingBiospecimen
83
scmC-seq Level 2Files contain scmC-seq files containing aligned sequence data, as a BAM file.Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Mean Coverage, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short ReadsFALSESequencingscmC-seq Level 1
84
scATAC-seq Level 4Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, scATACseq Workflow Type, scATACseq Workflow Parameters Description, Workflow Version, Workflow LinkFALSESequencingscATAC-seq Level 3
85
scDNA-seq Level 1Single-cell DNA-seqComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Sequencing Batch ID, Library Layout, Nucleic Acid Source, Library Selection Method, Read Length, Library Preparation Kit Name, Library Preparation Kit Vendor, Library Preparation Kit Version, Adapter Name, Adapter Sequence, Base Caller Name, Base Caller Version, Flow Cell Barcode, Fragment Maximum Length, Fragment Mean Length, Fragment Minimum Length, Fragment Standard Deviation Length, Lane Number, Library Strand, Multiplex Barcode, Size Selection Range, Target Depth, To Trim Adapter Sequence, Adapter Content, Basic Statistics, Encoding, Kmer Content, Overrepresented Sequences, Per Base N Content, Per Base Sequence Content, Per Base Sequence Quality, Per Sequence GC Content, Per Sequence Quality Score, Per Tile Sequence Quality, Percent GC Content, Sequence Duplication Levels, Sequence Length Distribution, Total Reads, QC Workflow Type, QC Workflow Version, QC Workflow LinkFALSESequencingBiospecimen
86
scDNA-seq Level 2Alignment workflows downstream of scDNA-seq Level 1Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Alignment Workflow Type, Genomic Reference, Genomic Reference URL, Index File Name, Average Base Quality, Average Insert Size, Average Read Length, Mean Coverage, Pairs On Diff CHR, Total Reads, Proportion Reads Mapped, MapQ30, Total Uniquely Mapped, Total Unmapped reads,Proportion Reads Duplicated, Short Reads, Proportion Coverage 10x, Proportion Coverage 30X, Proportion Targets No Coverage, Proportion Base Mismatch, Proportion Mitochondrial Reads, Contamination, Contamination ErrorFALSESequencingscDNA-seq Level 1
87
Multiplexed CITE-seq Level 1Raw sequencing files for the multiplexed CITE-seq assayComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source,Cryopreserved Cells in Sample, Single Cell Isolation Method, Dissociation Method, Library Construction Method,Read Indicator, Read1, Read2, End Bias, Reverse Transcription Primer, Spike In, Spike In Concentration, Sequencing Platform, Total Number of Input Cells, Input Cells and Nuclei, Library Preparation Days from Index, Single Cell Dissociation Days from Index, Sequencing Library Construction Days from Index, Nucleic Acid Capture Days from Index, Protocol Link, Technical Replicate Group, Empty Well Barcode,Well Index,Feature Reference Id, Associated mRNA Library Data File ID, Single Cell Barcode Method Applied, Feature Barcode Library Type, Barcode Folder Synapse ID, Barcode Folder File ListFALSESequencingBiospecimen
88
Multiplexed CITE-seq Level 2Alignment workflows downstream of Multiplexed CITE-seq Level 1Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Associated mRNA Library Data File ID, scRNAseq Workflow Type, Workflow Version, scRNAseq Workflow Parameters Description, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, Checksum, Whitelist Cell Barcode File Link, Cell Barcode Tag, UMI Tag, Applied Hard TrimmingFALSESequencingMultiplexed CITE-seq Level 1
89
Multiplexed CITE-seq Level 3Gene and Isoform expression filesComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Associated mRNA Library Data File ID, Data Category, Matrix Type, Linked Matrices, Cell Median Number Reads, Cell Median Number Genes, Cell Total, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Link, Workflow VersionFALSESequencingscRNA-seq Level 2
90
Multiplexed CITE-seq Level 4Data represents the relationships between cells derived from Level 3 expression data and shown as tSNE or UMAP coordinates per cell, plus all other cell-specific meta information (e.g., cell type)Component, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Associated mRNA Library Data File ID, scRNAseq Workflow Type, scRNAseq Workflow Parameters Description, Workflow Version, Workflow LinkFALSESequencingMultiplexed CITE-seq Level 3
91
Bulk Methylation-seq Level 1Raw data for bulk methylation sequencing, such as FASTQs and unaligned BAMsComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Nucleic Acid Source, Bisulfite Conversion, Sequencing Platform, Replicate Type, Bulk Methylation Assay Type, Total DNA InputFALSESequencingBiospecimen
92
Bulk Methylation-seq Level 2Aligned primary data for bulk methylation sequencing, such as gene expression matrix files, VCFs, etc.Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Alignment Workflow Url, Trimmer, Bulk Methylation Genomic Reference, Genomic Reference URL, Index File Name, Alignment Workflow Type, Duplicate Removal Software, Mean Coverage, Library Layout, Average Base Quality, Average Insert Size, Average Read Length, Contamination, Contamination Error, Pairs On Diff CHR, Total Reads, Total Uniquely Mapped, Total Unmapped reads, Proportion Reads Duplicated, Proportion Reads Mapped, Proportion Targets No Coverage, Proportion Base Mismatch, Short Reads, Proportion of Minimum CpG Coverage 10X, Proportion Coverage 30XFALSESequencingBulk Methylation-seq Level 1, Biospecimen
93
Bulk Methylation-seq Level 3Sample level summary data for bulk methylation sequencing, such as t-SNE plot coordinates, etc.Component, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID,DMC Calling Tool, DMC Calling Workflow URL, DMR Calling Tool, DMR Calling Workflow URL, pUC19 methylation ratio, Lambda methylation ratio, DMC data file format, DMR data file FormatFALSESequencingBulk Methylation-seq Level 2, Biospecimen
94
Imaging Level 1Raw imaging dataComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Imaging Assay Type, Protocol Link, Software and Version, Commit SHA, Pre-processing Completed, Pre-processing Required, CommentFALSEAssayBiospecimen
95
Imaging Level 2Raw and pre-processed image dataComponent, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance,WorkingDistanceUnit, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVXUnit, FOVY, FOVYUnit, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, PhysicalSizeZ, PhysicalSizeZUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelType, MERFISH Positions File, MERFISH Codebook FileFALSEAssayImaging Level 1
96
MERFISH Positions FileThe positions file is an auxiliary MERFISH file that describes the location of bead positions in the assay.FALSEAssay
97
MERFISH Codebook FileThe codebook is an auxiliary MERFISH file that describes how each grouping of bits is converted to a gene name.FALSEAssay
98
Imaging Level 3 SegmentationObject segmentationsComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Data File ID, Imaging Segmentation Data Type, Parameter file, Software and Version, Commit SHA, Imaging Object Class, Number of ObjectsFALSEAssayImaging Level 2
99
Imaging Level 3 ImageQuality controlled imaging dataComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Imaging Assay Type, Protocol Link,Software and Version, Microscope, Objective, NominalMagnification, LensNA, WorkingDistance, Immersion, Pyramid, Zstack, Tseries, Passed QC, Comment, FOV number, FOVX, FOVY, Frame AveragingFALSEAssayImaging Level 3 Channels, Imaging Level 2
100
10x Visium Spatial Transcriptomics - RNA-seq Level 1Files contain raw RNA-seq data associated with spot/slide data.Component, Filename, Run ID, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Read Indicator, Spatial Read1, Spatial Read2, Spatial Library Construction Method, Library Preparation Days from Index, Sequencing Library Construction Days from Index, End Bias, Reverse Transcription Primer, Sequencing Platform, Capture Area, Protocol Link, Slide Version, Slide ID, Image Re-orientation, Permeabilization Time, RIN, DV200FALSESpatial TranscriptomicsBiospecimen
101
10x Visium Spatial Transcriptomics - RNA-seq Level 2Alignment workflows downstream of Spatial Transcriptomics RNA-seq Level 1.Component, Filename, File Format, Checksum,HTAN Parent Data File ID, HTAN Data File ID, UMI Tag, Whitelist Spatial Barcode File Link, Spatial Barcode Tag, Applied Hard Trimming, Workflow Version, Workflow Link, Genomic Reference, Genomic Reference URL, Genome Annotation URL, HTAN Parent Biospecimen ID, Run ID, Capture AreaFALSESpatial Transcriptomics10x Visium Spatial Transcriptomics - RNA-seq Level 1
102
10x Visium Spatial Transcriptomics - Auxiliary FilesAuxiliary data associated with spot/slide analysis (aligned Images, quality control files, etc) from Spatial Transcriptomics.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Visium File Type, Slide ID, Capture Area, Workflow Version, Workflow LinkFALSESpatial Transcriptomics10x Visium Spatial Transcriptomics - RNA-seq Level 1, 10x Visium Spatial Transcriptomics - RNA-seq Level 2
103
10x Visium Spatial Transcriptomics - RNA-seq Level 3Processed data files based on Spatial Transcriptomics RNA-seq Level 2 and Spatial Transcriptomics Auxiliary files.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Visium File Type, Workflow Version, Workflow Link, Capture Area, Spots under tissue, Mean Reads per Spatial Spot, Median Number Genes per Spatial Spot, Sequencing Saturation, Proportion Reads Mapped, Proportion Reads Mapped to Transcriptome, Median UMI Counts per SpotFALSESpatial Transcriptomics10x Visium Spatial Transcriptomics - RNA-seq Level 2, 10x Visium Spatial Transcriptomics - Auxiliary Files
104
10x Visium Spatial Transcriptomics - RNA-seq Level 4Processed data files based on Spatial Transcriptomics RNA-seq Level 3.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Run ID, Workflow Version, Workflow Link, Visium Workflow Type, Visium Workflow Parameters DescriptionFALSESpatial Transcriptomics10x Visium Spatial Transcriptomics - RNA-seq Level 3
105
Visium File TypeThe file type generated for the visium experiment.reference png, reference jpg, json scale factors, probe dataset csv, qc result html, filtered mex, unfiltered mex, tissue_positions, barcodes, features, fiducial image png, fiducial image jpg, detected image png, detected jpg, high res image, low res image, json scale factors, probe dataset csvTRUESpatial Transcriptomics
106
Run IDA unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow.TRUESpatial Transcriptomics
107
Capture AreaArea (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1.A, B, C, D, A1, B1, C1, D1FALSESpatial Transcriptomics
108
Slide VersionVersion of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts.V1, V2, V3, V4FALSESpatial Transcriptomics
109
Slide IDFor Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide.FALSESpatial Transcriptomics
110
Image Re-orientationTo ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation.TRUE, FALSEFALSESpatial Transcriptomics
111
Permeabilization TimeFixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes.FALSESpatial Transcriptomics
112
Whitelist Spatial Barcode File LinkLink to file listing all possible spatial barcodes. URLTRUESpatial Transcriptomics
113
Spatial Barcode TagSAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z)TRUESpatial Transcriptomics
114
Spatial Barcode OffsetOffset in sequence for spot barcode read (in bp): numberTRUESpatial Transcriptomics
115
Spatial Barcode LengthLength of spot barcode read (in bp): numberTRUESpatial Transcriptomics
116
Spatial Read1Read 1 content descriptioncDNA, Spatial Barcode and UMITRUESpatial Transcriptomics
117
Spatial Read2Read 2 content descriptioncDNA, Spatial Barcode and UMITRUESpatial Transcriptomics
118
Spatial Library Construction MethodProcess which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711]Smart-seq2, Smart-SeqV4, 10xV1.0, 10xV1.1, 10xV2, 10xV3,10xV3.1, Drop-seq, inDropsV2, inDropsV3, TruDrop, Nextera XTTRUESpatial Transcriptomics
119
Spatial Barcode and UMISpot and transcript identifiersSpatial Barcode Offset, Spatial Barcode Length, UMI Barcode Offset, UMI Barcode LengthTRUESpatial Transcriptomicsnum
120
Mean Reads per Spatial SpotThe number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.TRUESpatial Transcriptomicsnum
121
Visium Workflow TypeGeneric name for the workflow used to analyze the visium data set.TRUESpatial Transcriptomics
122
Visium Workflow Parameters DescriptionParameters used to run the workflow..TRUESpatial Transcriptomics
123
Spots under tissueThe number of barcodes associated with a spot under tissue.TRUESpatial Transcriptomicsnum
124
Median UMI Counts per SpotThe median number of UMI counts per tissue covered spot.TRUESpatial Transcriptomicsnum
125
Sequencing SaturationThe fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene).TRUESpatial Transcriptomics
126
Proportion Reads Mapped to TranscriptomeFraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.TRUESpatial Transcriptomics
127
Median Number Genes per Spatial SpotThe median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.TRUESpatial Transcriptomicsnum
128
NanoString GeoMx DSP Spatial Transcriptomics Level 1Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Synapse ID of GeoMx DSP PKC File, GeoMx DSP NGS Sequencing Platform, GeoMx DSP NGS Library Selection Method, GeoMx DSP NGS Library Preparation Kit Name, GeoMx DSP Library Preparation Kit Vendor, GeoMx DSP Library Preparation Kit Version, Synapse ID of GeoMx Lab Worksheet File, Software and VersionFALSESpatial TranscriptomicsBiospecimen, NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
129
GeoMx DSP Assay TypeThe assay type which was used for the GeoMx DSP pipeline.RNA nCounter, Protein nCounter, Protein NGS, RNA NGSTRUESpatial Transcriptomics
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Synapse ID of GeoMx DSP PKC FileThe Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values.TRUESpatial Transcriptomicslist::regex match syn\d+
131
GeoMx DSP NGS Sequencing PlatformA platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument.FALSESpatial Transcriptomics
132
GeoMx DSP NGS Library Selection MethodHow RNA molecules are isolated.FALSESpatial Transcriptomics
133
GeoMx DSP NGS Library Preparation Kit NameName of Library Preparation Kit. StringFALSESpatial Transcriptomics
134
GeoMx DSP Library Preparation Kit VendorVendor of Library Preparation Kit. StringFALSESpatial Transcriptomics
135
GeoMx DSP Library Preparation Kit VersionVersion of Library Preparation Kit. StringFALSESpatial Transcriptomics
136
Synapse ID of GeoMx Lab Worksheet FileSynapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values.FALSESpatial Transcriptomicslist::regex match syn\d+
137
NanoString GeoMx DSP Spatial Transcriptomics Level 3Files contain processed data from the NanoString GeoMx DSP Pipeline. This level depends on GeoMx Level 1 and Imaging Level 2.Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, GeoMx DSP Assay Type, Synapse ID of GeoMx DSP ROI Segment Annotation File, GeoMx DSP Unique Probe Count, GeoMx DSP Unique Target Count, GeoMx DSP Genomic Reference, Matrix Type, GeoMx DSP Workflow Type, GeoMx DSP Workflow Parameter Description, GeoMx DSP Workflow LinkFALSESpatial TranscriptomicsNanoString GeoMx DSP Spatial Transcriptomics Level 1, Imaging Level 2, NanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
138
Synapse ID of GeoMx DSP ROI Segment Annotation FileSynapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment.TRUESpatial Transcriptomicslist::regex match syn\d+
139
GeoMx DSP Genomic ReferenceExact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMxFALSESpatial Transcriptomicsnum
140
GeoMx DSP Unique Probe CountTotal number of unique probes reported.FALSESpatial Transcriptomicsnum
141
GeoMx DSP Unique Target CountTotal number of unique genes reported.FALSESpatial Transcriptomicsnum
142
GeoMx DSP Workflow TypeGeneric name for the workflow used to analyze the GeoMx DSP data set.FALSESpatial Transcriptomics
143
GeoMx DSP Workflow Parameter DescriptionParameters used to run the GeoMx DSP workflow.FALSESpatial Transcriptomics
144
GeoMx DSP Workflow LinkLink to workflow or command. DockStore.org recommended. URLFALSESpatial Transcriptomics
145
NanoString GeoMx DSP ROI RCC Segment Annotation MetadataGeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. HTAN Parent Biospecimen ID, Scan name, ROI name, Segment name, ROI X Coordinate,ROI Y Coordinate, Tags, QC status, Scan Height, Scan Width, Scan Offset X, Scan Offset Y, Binding Density, Positive norm factor, Surface area, Nuclei count, Tissue StainFALSEAssay
146
Scan nameGeoMx Scan name (as appears in Segment Summary)TRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
147
ROI nameROI name (application generated). For Xenium this is referred to as the “region name”TRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
148
Segment nameName given to segment at time of generationTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
149
TagsUnique descriptor of a variable group (ie. MAPK+)TRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
150
ROI X CoordinateX location within the imageTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
151
ROI Y CoordinateY location within the imageTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
152
QC statusROI quality control flag as reported by the applicationFALSENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
153
Scan HeightHeight of the scan for GeoMx AnalysisTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
154
Scan WidthWidth of the scan for GeoMx AnalysisTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
155
Scan Offset XOffset X of the scan for GeoMx AnalysisTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
156
Scan Offset YOffset Y of the scan for GeoMx AnalysisTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
157
Binding DensityThe binding density as reported by the applicationFALSENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
158
Positive norm factorThe Positive Control Normalization factor calculated using pos-hyb controlsFALSENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
159
Surface areaSurface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region AreaTRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
160
Nuclei countNumber of nuclei detected in the segment (if applicable)TRUENanoString GeoMx DSP ROI RCC Segment Annotation Metadata, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata
161
Tissue Staine.g. CD45 or PanCK (if masking was performed)FALSENanoString GeoMx DSP ROI RCC Segment Annotation Metadata
162
NanoString GeoMx DSP ROI DCC Segment Annotation MetadataGeoMx ROI and Segment Metadata Attributes. The assayed biospecimen should be reported one per row with the associated ROI coordinates. HTAN Parent Biospecimen ID, Scan name, Slide name, ROI name, Segment name, ROI X Coordinate,ROI Y Coordinate, Tags, Scan Height, Scan Width, Scan Offset X, Scan Offset Y, Surface area, Nuclei count, Sequencing Saturation, MapQ30, Raw reads, Stitched reads, Aligned reads, Deduplicated reads, In Situ Negative median, Biological probe medianFALSEAssay
163
Slide nameSimilar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary).FALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
164
Raw readsReads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file. FALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
165
Stitched readsRepresents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned readsFALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
166
Aligned readsIs a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets.FALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
167
Deduplicated readsIs the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data.FALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
168
In Situ Negative medianIs the median of all negative control probes for a given segment. A measure of signal to background for each segment.FALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
169
Biological probe medianIs the median count from all probes except the negative control probes. A measure of signal to background for each segmentFALSENanoString GeoMx DSP ROI DCC Segment Annotation Metadata
170
HI-C-seq Level 1Unaligned sequence dataComponent, HTAN Parent Biospecimen ID, HTAN Data File ID, Filename, File Format, Genomic Reference, Sequencing Platform, Nucleic Acid Source, Technical Replicate Group, Transposition Reaction, Crosslinking Condtion, DNA Digestion Condition, Nuclei Permeabilization Method, Ligation Condition, Biotin Enrichment, DNA Input Amount, Total Reads, Protocol LinkFALSESequencingBiospecimen
171
HI-C-seq Level 2Aligned read pairs, contact matrixComponent, HTAN Data File ID, HTAN Parent Data File ID, Filename, File Format, Genomic Reference, Aligned Read Length, Tool, Resolution, Normalization MethodFALSESequencingHI-C-seq Level 1
172
HI-C-seq Level 3Summary data for the HI-C-seq assay.Component, HTAN Parent Data File ID, HTAN Data File ID, Filename, File Format, Genomic Reference, Stripe Calling, Loop Window, Stripe Window, Loop CallingFALSESequencingHI-C-seq Level 2
173
Crosslinking CondtionDetailed condition for DNA crosslinkingTRUESequencing
174
DNA Digestion ConditionEnzymes and treatment length/temperature for genome digestionTRUESequencing
175
Nuclei Permeabilization MethodDetergent and treatment condition for nuclei permeabilization and crosslinking softeningTRUESequencing
176
Ligation ConditionName of ligase and condition for proximity ligationTRUESequencing
177
Biotin EnrichmentWhether biotin is used for enriching ligation productYes, NoTRUESequencing
178
DNA Input AmountAmount of DNA for library construction, in nanograms.TRUESequencingint
179
ResolutionBinning size used for generating contact matrix, in basepair.TRUESequencing
180
Stripe CallingTool used for identifying architectural stripe-forming, interaction hotspots.MACS2, OtherTRUESequencing
181
Loop WindowBinning size used for calling significant dot interactions (loops)TRUESequencinglist like :: regex search -?\d+
182
Stripe WindowBinning size used for calling significant architectural stripes. Can be an integer or comma-separated list of integers indicating bin size and sliding window size if different.TRUESequencinglist like :: regex search -?\d+
183
Loop CallingTool used for identifying loop interactionsHiCCUPS, Cooltools, OtherTRUESequencing
184
Imaging Level 4Derived imaging data: Object-by-feature arrayComponent, Filename, File Format, HTAN Parent Data File ID, HTAN Parent Channel Metadata ID, HTAN Data File ID, Parameter file, Software and Version, Commit SHA,Number of Objects, Number of Features,Imaging Object Class, Imaging Summary StatisticFALSEAssayImaging Level 3 Channels
185
SRRS Imaging Level 2SRRS-specific HTAN raw and pre-processed image dataComponent, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Data File ID, Channel Metadata Filename, Imaging Assay Type, Protocol Link, Software and Version, Microscope, Objective, NominalMagnification, Pyramid, Zstack, Tseries, Passed QC, Frame Averaging, Image ID, DimensionOrder, PhysicalSizeX, PhysicalSizeXUnit, PhysicalSizeY, PhysicalSizeYUnit, Pixels BigEndian, PlaneCount, SizeC, SizeT, SizeX, SizeY, SizeZ, PixelTypeFALSEAssayBiospecimen
186
10X Genomics Xenium ISS ExperimentAll data pertaining to the 10X Genomics Xenium In-Situ Hybridization experimentComponent, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, Xenium Bundle Contents, Slide ID, ROI name, Panel Name, Protocol Link, Software and Version,Total Number of Cells, Total Number of Targets, Surface area, Experiment IF Channels, Transcripts per Cell, Percent of Transcripts within Cells, Decoded Transcripts, Xenium IF image HTAN File ID, Xenium HE image HTAN File IDFALSESpatial TranscriptomicsBiospecimen
187
Xenium Bundle ContentsA comma separated list of filenames within the Xenium bundle zip fileTRUESpatial Transcriptomics
188
Panel NameThe human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))TRUESpatial Transcriptomics
189
Total Number of CellsThe total number of cells analyzed on the flow cellTRUESpatial Transcriptomics
190
Total Number of TargetsRefers to the target of an assay. Can be genes/transcripts or probesTRUESpatial Transcriptomics
191
Experiment IF ChannelsA comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)TRUESpatial Transcriptomics
192
Transcripts per CellMean or Median transcript count per cell analyzed on the flow cell or slideTRUESpatial Transcriptomics
193
Percent of Transcripts within CellsThe percentage of transcripts assigned to assayed cellsTRUESpatial Transcriptomics
194
Decoded TranscriptsIn Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2).TRUESpatial Transcriptomics
195
Xenium IF image HTAN File IDThe HTAN Data File ID of a Imaging Level 2 fileFALSESpatial Transcriptomics
196
Xenium HE image HTAN File IDThe HTAN Data File ID of a Imaging Level 2 fileFALSESpatial Transcriptomics
197
RPPA Level 2Array based protemics. Each dilution curve of spot intensities is fitted using the monotone increasing B-spline model in the SuperCurve R package. This fits a single curve using all the samples on a slide with the signal intensity as the response variable and the dilution steps as independent variables. The fitted curve is plotted with the signal intensities on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic purposes.Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, HTAN RPPA Antibody Table, Assay Type, Protocol Link, Software and VersionFALSEAssayBiospecimen
198
HTAN RPPA Antibody TableA table containing antibody level metadata for RPPAHTAN RPPA Antibody Table ID, Filename, File Format, Ab Name Reported on Dataset, GENCODE Gene Symbol Target, UNIPROT Protein ID Target, Phosphoprotein Flag, Vendor, Catalog Number, Internal Ab ID, Species, RPPA Dilution, Phospho Site, RPPA Validation Status, Clone, Clonality, Antibody NotesTRUERPPA Level 2
199
RPPA Level 3Level 3 Reverse Phase Protein Array (RPPA) data contains intra-batch normalized intensities.Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Software and Version, Normalization MethodFALSEAssayBiospecimen
200
RPPA Level 4Level 4 Reverse Phase Protein Array (RPPA) data contains intra-batch corrected intensities.Component, Filename, File Format, HTAN Participant ID, HTAN Parent Biospecimen ID, HTAN Parent Data File ID, HTAN Data File ID, Assay Type, Batch Correction MethodFALSEAssayRPPA Level 2
201
Nanostring CosMx SMI ExperimentRNA and Protein Panel assays applied as part of Nanostring CosMx Spatial Molecular Imager (SMI)Component, Filename, File Format, HTAN Parent Biospecimen ID, HTAN Data File ID, CosMx Bundle Contents, Slide ID, CosMx Assay Type, Panel Name, Protocol Link, Software and Version, Total Number of Cells, Total Number of Targets, Number of FOVs, Surface area, Experiment IF Channels, Transcripts per Cell, Percent of Transcripts within Cells, Mean Total Transcripts per Area, Unique Genes, Total Negative Probe CountsFALSESpatial TranscriptomicsBiospecimen
202
CosMx Bundle ContentsA comma separated list of filenames within the CosMx bundle zip fileTRUESpatial Transcriptomics