National Institute of Mental Health Data Archive (NDA) Sign In
National Institute of Mental Health Data Archive (NDA) Sign In

Success! An email is on its way!

Please check your email to complete the linking process. The link you receive is only valid for 30 minutes.

Check your spam or junk folder if you do not receive the email in the next few minutes.

Warning Notice This is a U.S. Government computer system, which may be accessed and used only for authorized Government business by authorized personnel. Unauthorized access or use of this computer system may subject violators to criminal, civil, and/or administrative action. All information on this computer system may be intercepted, recorded, read, copied, and disclosed by and to authorized personnel for official purposes, including criminal investigations. Such information includes sensitive data encrypted to comply with confidentiality and privacy requirements. Access or use of this computer system by any person, whether authorized or unauthorized, constitutes consent to these terms. There is no right of privacy in this system.
Create or Link an Existing NDA Account
NIMH Data Archive (NDA) Sign In or Create An Account
Update Password

You have logged in with a temporary password. Please update your password. Passwords must contain 8 or more characters and must contain at least 3 of the following types of characters:

  • Uppercase
  • Lowercase
  • Numbers
  • Special Characters limited to: %,_,!,@,#,$,-,%,&,+,=,),(,*,^,:,;

Subscribe to our mailing list

Mailing List(s)
Email Format

You are now leaving the NIMH Data Archive (NDA) web site to go to:

Click on the address above if the page does not change within 10 seconds.


NDA is not responsible for the content of this external site and does not monitor other web sites for accuracy.

Accept Terms
Data Access Terms - Decline Terms

Are you sure you want to cancel? This will decline terms and you will not be authorized for access.

Filter Cart
No filters selected
Value Range
Data Structures with shared data
No filters have been selected
Switch User

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.
View Change History
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 :: 1260 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; 2 1=Forward; 2=Reverse
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 Recommended Data file 1
data_file1_type String 300 Recommended type of data file 1
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

Please email the The NDA Help Desk with any questions.