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ATAC Sequencing

0 Shared Subjects

Metadata information about Assay for Transposase-accessible chromatin with sequencing (ATAC-seq) experiment/project. ATAC-seq determines chromatin accessibility across the genome can can help determine how chromatin packaging and other factors affect gene expression.
Omics
Omics
05/23/2022
atac_seq01
03/15/2024
View Change History
01
Definition
Submission Template
Query Element Name Data Type Size Required Description Value Range Notes Aliases
subjectkey GUID Required The NDAR Global Unique Identifier (GUID) for research subject NDAR*
src_subject_id String 20 Required Subject ID how it's defined in lab/project
interview_date Date Required Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_age Integer Required Age in months at the time of the interview/test/sampling/imaging. 0::1440 Age 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.
sex String 20 Required Sex of subject at birth M;F; O; NR M = Male; F = Female; O=Other; NR = Not reported
experiment_id Integer Required ID for the Experiment/settings/run
cellid String 4,000 Recommended Unique identifier of cells
samplesubtype Integer Recommended Subtype of sample, whether it is cells, nuclei, or bulk 1::3 1=Cell; 2=Nucleus; 3=Bulk
libraryid String 4,000 Recommended Library ID as provided by the lab
gen_software String 4,000 Recommended Name of the software used on sequencing platform
softwareversion String 4,000 Recommended Version number of the software used
referenceset Integer Recommended A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data 1::5; -99 1=1000 Genomes phase 3; 2=GRCh38; 3=GRCh37; 4=MMUL1.0; 5=HRC; -99=Other
otherreferenceset String 4,000 Recommended A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data
librarybatch String 4,000 Recommended Batch library was prepared in
sequencingbatch String 4,000 Recommended Batch library was sequenced in
libraryselection Integer Recommended The general strategy by which the library was prepared 1::37; -88; -99 1=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
libraryconstructionprotocol Integer Recommended Method used to construct the sequence library 1::30; -99 1=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; -99=Other
otherlibraryconstructprotocol String 4,000 Recommended Other type of library construction protocol not listed otherlibraryconstructionprotocol
librarysource Integer Recommended The type of source material that is being sequenced 1; 2; -99 1=Genomic; 2=Genomic single cell; -99=Other
otherlibrarysource String 4,000 Recommended Other library source not listed
readlength Float Recommended The length of the read
librarylayout Integer Recommended If the library is paired-end or single-end 1; 2 1=Single; 2=Paired-end
totalreads Integer Recommended Total number of sequencing reads from a library
numbercells Integer Recommended Number of cells or nuclei sequenced
readstrandorigin Integer Recommended The strand from which the read originates in a strand-specific protocol 1::4; 999 1=Forward; 2=Reverse; 3=Unstranded; 4=First-strand; 999=Missing
isstranded Integer Recommended Whether or not the library is stranded. 0; 1 0=No; 1=Yes
pcrcycles Integer Recommended Number of PCR cycles to amplify transposased DNA fragments
meancoverage Float Recommended Total number of bases covered by ATAC-seq reads/size of genome
transposasebatch String 4,000 Recommended Transposition reaction batch
meangccontent Float Recommended Mean GC content per sample
data_file1 File 255 Recommended Data file 1
data_file1_type String 300 Recommended type of data file 1
hemisphere Float Recommended Hemisphere: 1 right / 0 left 0;1;999 0=Left; 1=Right; 999=Unknown
study String 100 Recommended Study; The code for each individual study
brodmann_area String 20 Recommended A segmentation of the cerebral cortex on the basis of cytoarchitecture
readlength_max Float Recommended The maximum length of the read
readlength_min Float Recommended The minimum length of the read
sequencingplatform Integer Recommended Sequencing platform 0::2; 999 0=HiSeq2000; 1=HiSeq2500; 2=HiSeq4000; 999=Missing
filename String 100 Recommended File name
hcdi_postmortem_int_hr Integer Recommended Post-mortem interval in hours
hcdi_tissue Integer Recommended Organ or tissue of origin for cells if not listed 1::76; -77; -88; -99 1=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
library_prep_batch String 255 Recommended Sequencing library batch
platform String 255 Recommended Name of particular experiment platform
sample_id_biorepository String 100 Recommended Biorepository Sample ID
assay Integer Recommended The technology used to generate the data in this file 0::15; 999 0=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
grant String 20 Recommended Grant number including activity code, institute code, and serial number (e.g. U01MH103392)
hcdi_organ Integer Recommended Organ of origin for cells if applicable 1::19; -99 1=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
hcdi_organ_other String 100 Recommended Other organ for cell origin if not listed
samplebarcode String 20 Recommended The nucleotide sequence of the sample barcode used to identify cells from a single sample in cell hashing or multiplexing assays.
sequencingbarcodeindex Integer Recommended Sequencing barcode index 0::7; 999 0=N701; 1=N702; 2=N703; 3=N704; 4=N705; 5=N706; 6=N707; 7=N708; 999=missing
specimenid_renamed Integer Recommended Was the specimenid renamed? 0;1; 999 0=No; 1=Yes; 999=Missing
Data Structure

This page displays the data structure defined for the measure identified in the title and structure short name. The table below displays a list of data elements in this structure (also called variables) and the following information:

  • Element Name: This is the standard element name
  • Data Type: Which type of data this element is, e.g. String, Float, File location.
  • Size: If applicable, the character limit of this element
  • Required: This column displays whether the element is Required for valid submissions, Recommended for valid submissions, Conditional on other elements, or Optional
  • Description: A basic description
  • Value Range: Which values can appear validly in this element (case sensitive for strings)
  • Notes: Expanded description or notes on coding of values
  • Aliases: A list of currently supported Aliases (alternate element names)
  • For valid elements with shared data, on the far left is a Filter button you can use to view a summary of shared data for that element and apply a query filter to your Cart based on selected value ranges

At the top of this page you can also:

  • Use the search bar to filter the elements displayed. This will not filter on the Size of Required columns
  • Download a copy of this definition in CSV format
  • Download a blank CSV submission template prepopulated with the correct structure header rows ready to fill with subject records and upload

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