NDAABCDCCFOAINIAAADAAMP SCZHEALNBBPEC

Data Structure

RNA Sequencing

Version 011119 Shared Subjects
Short Name: rna_seq01
Data Type: Genomics
Categories: Omics

Metadata information about a RNA-sequencing (RNA-seq) experiment/project

Query this Structure
DOWNLOADS
Definition
Submission Template

A Collection's submission must not be cumulative.

85 Elements

Name
Type
Required
Description
Value Range
Notes
subjectkeyGUIDRequiredThe NDAR Global Unique Identifier (GUID) for research subjectNDAR*
src_subject_idStringRequiredSubject ID how it's defined in lab/project
interview_dateDateRequiredDate on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_ageIntegerRequiredAge in months at the time of the interview/test/sampling/imaging.0::1440Age is rounded to chronological month. If the research participant is 15-days-old at time of interview, the appropriate value would be 0 months. If the participant is 16-days-old, the value would be 1 month.
sexStringRequiredSex of subject at birthM;F; O; NRM = Male; F = Female; O=Other; NR = Not reported
experiment_idIntegerRequiredID for the Experiment/settings/run
cellidStringRecommendedUnique identifier of cells
samplesubtypeIntegerRecommendedSubtype of sample, whether it is cells, nuclei, or bulk1::31=Cell; 2=Nucleus; 3=Bulk
libraryidStringRecommendedLibrary ID as provided by the lab
gen_softwareStringRecommendedName of the software used on sequencing platform
softwareversionStringRecommendedVersion number of the software used
referencesetIntegerRecommendedA set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data1::5; -991=1000 Genomes phase 3; 2=GRCh38; 3=GRCh37; 4=MMUL1.0; 5=HRC; -99=Other
otherreferencesetStringRecommendedA set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data
librarybatchStringRecommendedBatch library was prepared in
sequencingbatchStringRecommendedBatch library was sequenced in
libraryselectionIntegerRecommendedThe general strategy by which the library was prepared1::37; -88; -991=Random; 2=PCR Random PCR; 3=RT-PCR; 4=HMPR; 5=MF; 6=repeat fractionation; 7=size fractionation; 8=MSLL; 9=cDNA; 10=cDNA random priming; 11=cDNA oligo-dT; 12=PolyA; 13=Oligo-dT; 14=Inverse rRNA; 15=ChIP; 16=MNase; 17=DNase; 18=Hybrid selection; 19=Reduced representation; 20=Restriction digest; 21=5-methylcytidine antibody; 22=MBD2 protein methyl-CpG binding domain; 23=CAGE; 24=RACE; 25=MDA; 26=padlock probes capture method; 27=cell hashing; 28=DHA library construction; 29=EndItDNAEndRepairKit; 30=KapaHyperPrep; 31=IncRNAenrichment; 32=MULTIseq; 33=PCR-free; 34=rRNA depletion; 35=SPLITseq; 36=STARRseq; 37=SureCell; -99=Other; -88=Unspecified
libraryconstructionprotocolIntegerRecommendedMethod used to construct the sequence library1::31; -991=SMART-seq; 2=SMART-seq2; 3=SMART-seq3; 4=SMART-seq4; 5=STRT-seq; 6=STRT-seq-C1; 7=STRT-seq-2i; 8=Quartz-seq; 9=Quartz-seq2; 10=CEL-seq; 11=CEL-seq2; 12=10x Chromium Single Cell 3' V3 FeatureBarcoding; 13=10x Chromium Single Cell 3' V2 and V3 GE; 14=10x Chromium Single Cell 3' V1 GE; 15=10x Chromium Single Cell 5' VDJ; 16=10x Chromium Single Cell 5' GE; 17=SureCell 3' WTA for ddSEQ; 18=MARS-seq / MARS-seq2.0; SCRB-seq / mcSCRB-seq; 18=Drop-seq / Seq-Well; 19=scifi-RNA-seq; 20=Microwell-seq; 21=BD Rhapsody; 22=sci-RNA-seq3; 23=sci-RNA-seq; 24=Seq-Well S3; 25=Tang 2009; 26=SPLiT-seq; 27=inDrop; 28=NEBNext; 29=NexteraXT; 30=Omni-ATAC; 31=10x Visium Gene Expression protocol; -99=Other
otherlibraryconstructprotocolStringRecommendedOther type of library construction protocol not listed
librarysourceIntegerRecommendedThe type of source material that is being sequenced1; 2; -991=Genomic; 2=Genomic single cell; -99=Other
otherlibrarysourceStringRecommendedOther library source not listed
readlengthFloatRecommendedThe length of the read
librarylayoutIntegerRecommendedIf the library is paired-end or single-end1; 21=Single; 2=Paired-end
totalreadsIntegerRecommendedTotal number of sequencing reads from a library
numbercellsIntegerRecommendedNumber of cells or nuclei sequenced
readstrandoriginIntegerRecommendedThe strand from which the read originates in a strand-specific protocol1::4; 9991=Forward; 2=Reverse; 3=Unstranded; 4=First-strand; 999=Missing
isstrandedIntegerRecommendedWhether or not the library is stranded.0; 10=No; 1=Yes
libraryversionStringRecommendedLibrary Version: for example, rnaSeq 10x library version
validbarcodereadsStringRecommendedFraction of reads with cell barcodes that match the whitelist
mediangenesIntegerRecommendedThe median number of genes detected (with nonzero UMI counts) across all cell-associated barcodes
medianumisIntegerRecommendedThe median number of total Unique Molecular Identifier (UMI) counts across all cell-associated barcodes
gen_rinFloatRecommendedRNA Integrity Number
rnabatchStringRecommendedBatch in which RNA sample was isolated
ribozero_batchStringRecommendedRibozero treatment batch
data_file1FileRecommendedData file 1
data_file1_typeStringRecommendedtype of data file 1
hcdi_tissueIntegerRecommendedOrgan or tissue of origin for cells if not listed1::76; -77; -88; -991=Amygdala; 2=Amygdaloid complex; 3=Anterior cingulate cortex; 4=Blood; 5=Bone marrow; 6=Buccal Mucosa; 7=Buffy Coat; 8=Caudate nucleus; 9=Cecum derived fecal material; 10=Cerebellar cortex; 11=Cerebellum; 12=Cerebral cortex; 13=Cortical plate; 14=Dorsal pallium; 15=Dorsal Root Ganglion; 16=Dorsolateral prefrontal cortex; 17=Dorsomedial prefrontal cortex; 18=Embryonic tissue; 19=Fecal material; 20=Forebrain; 21=Frontal cortex; 22=Frontal lobe; 23=Frontal pole; 24=Hippocampus; 25=Head of caudate nucleus; 26=Inferior frontal gyrus; 27=Inferior temporal cortex; 28=Inferior temporal gyrus; 29=Inferolateral temporal cortex; 30=Insular cortex; 31=Left cerebral hemisphere; 32=Livermedial dorsal nucleus of thalamus; 33=Medial frontal cortex; 34=Medial ganglionic eminence; 35=Medial orbital frontal cortex; 36=Medial prefrontal cortex; 37=Meninges; 38=Midbrain; 39=Middle frontal gyrus; 40=Middle temporal gyrus; 41=Nerve tissue; 42=Nucleus accumbens; 43=Occipital lobe; 44=Occipital visual cortex; 45=Olfactory neuroepithelium; 46=Orbitofrontal cortex; 47=Parahippocampal gyrus; 48=Parietal cortex; 49=Plasma; 50=Posterior cingulate cortex; 51=Posteroinferior parietal cortex; 52=Posterior inferior parietal cortex; 53=Posterior superior temporal cortex; 54=Precentral gyrus; 55=Prefrontal cortex; 56=Primary auditory cortex; 57=Primary motor cortex; 58=Primary somatosensory cortex; 59=Primary tumor; 60=Primary visual cortex; 61=Putamen; 62=Right cerebral hemisphere; 63=Serum; 64=Splenocyte; 65=Striatum; 66=Subgenual anterior cingulate cortex; 67=Subgenual cingulate cortex; 68=Superior parietal lobe; 69=Superior temporal gyrus; 70=Temporal cortex; 71=Temporal pole; 72=Thalamus; 73=Ventricular zone; 74=Ventrolateral prefrontal cortex; 75=VZ/SVZ; 76=Whole brain; -77=Unspecified; -88=Not Applicable; -99=Other
dlpfc_rna_isola_prepoperatorStringRecommendedOperator for DNA Isolation Preparation
flowcell_batchStringRecommendedMultiplex batch
flowcell_lane_aStringRecommendedFlowcell lane
flowcell_lane_bStringRecommendedFlowcell lane
flowcell_nameStringRecommendedflowcell identifier
hemisphereFloatRecommendedHemisphere: 1 right / 0 left0;1;9990=Left; 1=Right; 999=Unknown
rat280FloatRecommendedRatio of absorbance at 260nm and 280nm
sample_id_biorepositoryStringRecommendedBiorepository Sample ID
psych_enc_exclude_reasonStringRecommendedReason subject was excluded from study
flowcell_2StringRecommendedCMC_HBCC-specific flowcell identifier
flowcell_given_to_coreStringRecommendedFlowcell identifier
flowcell_idStringRecommendedFlowcell identifiermultiple flowcells separated by ::
flowcell_name_2StringRecommendedCMC_HBCC-specific flowcell name
studyStringRecommendedStudy; The code for each individual study
brodmann_areaStringRecommendedA segmentation of the cerebral cortex on the basis of cytoarchitecture
psych_enc_excludeIntegerRecommendedSubject excluded from study0;1;9990=No; 1=Yes; 999=Missing
ercc_addedIntegerRecommendedIndicates if ERCC spike-in pools were added to the background RNA0;1; 999 0=No; 1=Yes; 999=missing
librarykitIntegerRecommendedIllumina kit catalogue number0;1; 9990=Illumina RS-122-2301; 1=Kapa Hyper Prep Kit; 999=missing
librarytypeStringRecommendedThe type of library, in assays where samples are barcoded or hashed for multiplexing or each sample has multiple libraries amplified separately before pooled sequencing.
mappedreads_multimappedIntegerRecommendedMapped reads multimapped
mappedreads_primaryIntegerRecommendedMapped reads primary
nucleicacidsourceIntegerRecommendedSubtype of sample, whether it is bulk cell, bulk nuclei, single cell, single nucleus, sorted cells, or sorted nuclei.0::5; 9990=bulk cell; 1=bulk nuclei; 2=single cell; 3=single nucleus; 4=sorted cells; 5=sorted nuclei; 999=missing
readlength_maxFloatRecommendedThe maximum length of the read
readlength_minFloatRecommendedThe minimum length of the read
rnaseqidStringRecommendedID for RNAseq Assay
rrnarateIntegerRecommendedrRNA Rate0::11; 999 0=0.00%; 1=0.01%; 2=0.02%; 3=0.03%; 4=0.04%; 5=0.05%; 6=0.06%; 7=0.11%; 8=DNE; 9=average; 10=max; 11=std; 999=missing
samplebarcodeStringRecommendedThe nucleotide sequence of the sample barcode used to identify cells from a single sample in cell hashing or multiplexing assays.
sequencingplatformIntegerRecommendedSequencing platform0::2; 999 0=HiSeq2000; 1=HiSeq2500; 2=HiSeq4000; 999=Missing
tissuestateIntegerRecommendedState of tissue preservation0;1; 999 0=Flash frozen chunk; 1=Flash frozen chunk then isolated in trizol; 999=missing
celltypeStringRecommendedCell type
externalreferenceStringRecommendedExternal Data Reference
filenameStringRecommendedFile name
library_prep_batchStringRecommendedSequencing library batch
platformStringRecommendedName of particular experiment platform
assayIntegerRecommendedThe technology used to generate the data in this file0::15; 9990=ATACSeq; 1=CUT(and)Tag; 2=ChIPSeq; 3=GO-CaRT; 4=HI-C; 5=RNA-seq; 6=TMT quantitation; 7=bisulfiteSeq; 8=errBisulfiteSeq; 9=label free mass spectrometry; 10=methylationArray; 11=mirnaSeq; 12=oxBS-Seq; 13=scrnaSeq; 14=snpArray; 15=wholeGenomeSeq; 999=Missing
hcdi_organIntegerRecommendedOrgan of origin for cells if applicable1::19; -991=Lymph node; 2=Kidney; 3=Skin; 4=Mammary gland; 5=Nerves; 6=Brain; 7=Blood; 8=Breast; 9=Colon; 10=Lung; 11=Prostate; 12=Pancreas; 13=Ovary; 14=Spleen; 15=Bone marrow; 16=Bursa Of Fabricius; 17=Nose; 18=Cerebrospinal fluid; 19=Liver; -99=Other
ethnicityStringRecommendedEthnicity of participantHispanic or Latino; Not Hispanic or Latino; Unknown
psych_enc_datatypeIntegerRecommendedRNA data type0;1;999 0=lncRNA; 1=mRNA; 999=missing
rna_typeIntegerRecommendedRNA type0;1;999 0=rRNA-depleted; 1=total RNA; 999=missing
sequencing_assayIntegerRecommendedSequencing assay0::2;999 0=IsoSeq; 1=RNA-Seq; 2=SeqCap; 999=missing
submission_file_nameStringRecommendedSubmission file name
file_statusIntegerRecommendedStatus of files0;1;9990=Processed; 1=Raw; 999=Missing
data_file5_typeStringRecommendeddata file 5 type/description
data_file5FileRecommendedData file 5
visium_protocol_versionStringRecommendedProtocol version of the visium slides usedEx V1, V2, or other
loupe_versionStringRecommendedLoupe alignment version
fetal_ageIntegerRecommendedAge of the fetus (i.e., gestational age) in days0::322
fetal_age_typeIntegerRecommendedType of gestational age used for fetal_age1;21 = Postovulatory gestational age, defined as days since the last ovulation, expected term of 266 days; 2 = Postmenstrual gestational age, days since the last menstrual period, expected term of 280 days
differentiationdaysincultureIntegerRecommendedNumber of days in culture