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1 Numbers reported are subjects by age
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Format should be in the following format: Activity Code, Institute Abbreviation, and Serial Number. Grant Type, Support Year, and Suffix should be excluded. For example, grant 1R01MH123456-01A1 should be entered R01MH123456

Please select an experiment type below

Collection - Use Existing Experiment
To associate an experiment to the current collection, just select an axperiment from the table below then click the associate experiment button to persist your changes (saving the collection is not required). Note that once an experiment has been associated to two or more collections, the experiment will not longer be editable.

The table search feature is case insensitive and targets the experiment id, experiment name and experiment type columns. The experiment id is searched only when the search term entered is a number, and filtered using a startsWith comparison. When the search term is not numeric the experiment name is used to filter the results.
SelectExperiment IdExperiment NameExperiment Type
Created On
24HI-NGS_R1Omics02/16/2011
475MB1-10 (CHOP)Omics06/07/2016
490Discovery and CRISPR validation of genetic factors associated with antipsychotic-induced weight gain and cardiometabolic riskOmics07/07/2016
501PharmacoBOLD Resting StatefMRI07/27/2016
506PVPREFOmics08/05/2016
509ABC-CT Resting v2EEG08/18/2016
13Comparison of FI expression in Autistic and Neurotypical Homo SapiensOmics12/28/2010
18AGRE/Broad Affymetrix 5.0 Genotype ExperimentOmics01/06/2011
22Stitching PCR SequencingOmics02/14/2011
26ASD_MethylationOmics03/01/2011
29Microarray family 03 (father, mother, sibling)Omics03/24/2011
37Standard paired-end sequencing of BCRsOmics04/19/2011
38Illumina Mate-Pair BCR sequencingOmics04/19/2011
39Custom Jumping LibrariesOmics04/19/2011
40Custom CapBPOmics04/19/2011
41ImmunofluorescenceOmics05/11/2011
43Autism brain sample genotyping, IlluminaOmics05/16/2011
47ARRA Autism Sequencing Collaboration at Baylor. SOLiD 4 SystemOmics08/01/2011
53AGRE Omni1-quadOmics10/11/2011
59AGP genotypingOmics04/03/2012
60Ultradeep 454 sequencing of synaptic genes from postmortem cerebella of individuals with ASD and neurotypical controlsOmics06/23/2012
63Microemulsion PCR and Targeted Resequencing for Variant Detection in ASDOmics07/20/2012
76Whole Genome Sequencing in Autism FamiliesOmics01/03/2013
519RestingfMRI11/08/2016
90Genotyped IAN SamplesOmics07/09/2013
91NJLAGS Axiom Genotyping ArrayOmics07/16/2013
93AGP genotyping (CNV)Omics09/06/2013
106Longitudinal Sleep Study. H20 200. Channel set 2EEG11/07/2013
107Longitudinal Sleep Study. H20 200. Channel set 3EEG11/07/2013
108Longitudinal Sleep Study. AURA 200EEG11/07/2013
105Longitudinal Sleep Study. H20 200. Channel set 1EEG11/07/2013
109Longitudinal Sleep Study. AURA 400EEG11/07/2013
116Gene Expression Analysis WG-6Omics01/07/2014
131Jeste Lab UCLA ACEii: Charlie Brown and Sesame Street - Project 1Eye Tracking02/27/2014
132Jeste Lab UCLA ACEii: Animacy - Project 1Eye Tracking02/27/2014
133Jeste Lab UCLA ACEii: Mom Stranger - Project 2Eye Tracking02/27/2014
134Jeste Lab UCLA ACEii: Face Emotion - Project 3Eye Tracking02/27/2014
145AGRE/FMR1_Illumina.JHUOmics04/14/2014
146AGRE/MECP2_Sanger.JHUOmics04/14/2014
147AGRE/MECP2_Junior.JHUOmics04/14/2014
151Candidate Gene Identification in familial AutismOmics06/09/2014
152NJLAGS Whole Genome SequencingOmics07/01/2014
154Math Autism Study - Vinod MenonfMRI07/15/2014
155RestingfMRI07/25/2014
156SpeechfMRI07/25/2014
159EmotionfMRI07/25/2014
160syllable contrastEEG07/29/2014
167School-age naturalistic stimuliEye Tracking09/19/2014
44AGRE/Broad Affymetrix 5.0 Genotype ExperimentOmics06/27/2011
45Exome Sequencing of 20 Sporadic Cases of Autism Spectrum DisorderOmics07/15/2011
Collection - Add Experiment
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Your Collection is now in Data Analysis phase and exempt from biannual submissions. Analyzed data is still expected prior to publication or no later than the project end date.

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Collection Summary Collection Charts
Collection Title Collection Investigators Collection Description
PsychENCODE Consortium
Zhiping Weng; Mark Gerstein 
Established in 2015 by the National Institute of Mental Health (NIMH), the PsychENCODE Consortium (PEC) is a multi-site investigation of the genomic basis of neuropsychiatric diseases. The aim is to create a resource of mechanistic insights to guide future therapeutic development. Genomic influences on neural function are remarkably complex, characterized by a highly polygenic risk architecture and often located in the non-coding parts of the genome. A key objective of PEC is to delineate an enhanced framework of regulatory genomic elements associated with neuropsychiatric disorders. Multidisciplinary PEC teams are working to generate large-scale gene expression and regulatory data from human postmortem brains across several major psychiatric disorders. Brain tissue is characterized across multiple developmental stages and include bulk tissue, single cell, and sorted cell types. The goal is to map and functionally validate disease‐associated variants, regulatory elements, genes and cell types. Data from Phase I was presented in a collection of 11 papers published in Science, Science Translational Medicine, and Science Advances. This collection is summarized in the Science special issue "Revealing the brain's molecular architecture" . Phase II – which will enhance cellular and developmental resolution – is currently underway.
NIMH Data Archive
09/20/2023
The use of this data is limited to Health/Medical/Biomedical purposes, and does not include the study of population origins or ancestry (HMB). Requestor agrees to make results of studies using the data available to the larger scientific community (PUB). The use of this data includes methods development research (e.g. development and testing of software or algorithms).
PsychENCODE Consortium
Enrolling
No
$136,499,861.00
4,667
10.15154/1g4m-dy13
Loading Chart...
NIH - Extramural None



U01MH103340-01 Genetic variants affect brain gene expression and risks of psychiatric disorders 06/10/2014 05/31/2017 05/31/2017 Not Reported Not Reported UNIVERSITY OF ILLINOIS AT CHICAGO $2,464,072.00
U01MH103365-01 Gene regulatory elements and transcriptome in iPSCs and embryonic human cortex 06/15/2014 05/31/2017 05/31/2017 Not Reported Not Reported YALE UNIVERSITY $1,462,340.00
U01MH103339-01 Transcriptional and Epigenetic Signatures of Human Brain Development and Autism 06/15/2014 05/31/2017 05/31/2017 Not Reported Not Reported YALE UNIVERSITY $3,387,402.00
U01MH103392-01 Cis-Regulatory Epigenome Mappings in Schizophrenia 06/15/2014 05/31/2017 05/31/2017 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $1,830,695.00
U01MH103346-01 The USC PsychENCODE Project 06/15/2014 05/31/2017 05/31/2017 Not Reported Not Reported UNIVERSITY OF SOUTHERN CALIFORNIA $1,462,501.00
R21MH102791-01 Establishing comprehensive and quantitative maps of DNA methylation in the develo 08/01/2014 07/31/2016 07/31/2017 Not Reported Not Reported LIEBER INSTITUTE, INC. $595,750.00
P50MH106934-01 Functional Genomics of Human Brain Development 09/19/2014 07/31/2019 07/31/2019 Not Reported Not Reported YALE UNIVERSITY $2,969,187.00
R01MH105472-01 Decoding schizophrenia-From GWAS to functional regulatory variants 09/19/2014 06/30/2018 06/30/2018 Not Reported Not Reported DUKE UNIVERSITY $1,573,679.00
R21MH103877-01 GABA Epigenomes in Autism 09/26/2014 08/31/2016 08/31/2017 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $447,115.00
R21MH105881-01 Long non-coding RNAs in gene regulatory networks underlying Autism 12/01/2014 11/30/2016 11/30/2017 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $465,413.00
R01MH105898-01 RNA Sequencing of the Limbic System in Bipolar Disorder 09/01/2015 05/31/2019 02/28/2021 300 Not Reported JOHNS HOPKINS UNIVERSITY $3,137,397.00
R21MH105853-01 Decomposing cell type-specific marks in post-mortem human brain studies 09/03/2015 08/31/2017 08/31/2019 Not Reported Not Reported LIEBER INSTITUTE, INC. $508,750.00
R21MH109956-01 Characterizing the developing human brain transcriptome at single-base resolution 05/01/2016 04/30/2018 04/30/2019 Not Reported Not Reported LIEBER INSTITUTE, INC. $502,150.00
R01MH110920-01 1/2 Measuring translational dynamics and the proteome to identify potential brain biomakers for psychiatric disease 07/08/2016 04/30/2020 04/30/2021 Not Reported Not Reported UPSTATE MEDICAL UNIVERSITY $2,049,505.00
R01MH110905-01 2/2-Measuring translational dynamics and the proteome to identify potential brain biomarkers for psychiatric disease 07/08/2016 04/30/2020 04/30/2020 Not Reported Not Reported UNIVERSITY OF CHICAGO $1,092,180.00
R01MH110926-01 1/3 Integrative Genomic Analysis of Human Brain Development and Autism 07/21/2016 04/30/2020 04/30/2021 Not Reported Not Reported YALE UNIVERSITY $3,204,238.00
R01MH110928-01 3/3 Integrative Genomic Analysis of Human Brain Development and Autism 07/21/2016 04/30/2020 04/30/2020 Not Reported Not Reported UNIVERSITY OF CALIFORNIA, SAN FRANCISCO $1,294,456.00
R01MH109677-01 Risk genetic variants and cis regulation of gene expression in Bipolar Disorder 08/01/2016 05/31/2021 05/31/2021 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $2,617,098.00
R01MH110927-01 2/3 Integrative Genomic Analysis of Human Brain Development and Autism 08/10/2016 04/30/2020 04/30/2020 Not Reported Not Reported UNIVERSITY OF CALIFORNIA LOS ANGELES $2,073,628.00
R01MH110921-01 Molecular Profiling of Schizophrenia 09/01/2016 12/31/2020 12/31/2020 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $5,122,345.00
R01MH111721-01 Integrative Genomics of the Corticolimbic Circuit in Major Depressive Disorder 09/06/2017 05/31/2022 05/31/2024 400 Not Reported JOHNS HOPKINS UNIVERSITY $4,163,018.00
R01MH109715-01 Mapping the role of long noncoding RNAs in gene regulatory networks in schizophrenia 12/01/2017 11/30/2022 11/30/2024 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $3,982,639.00
R01MH117406-01 The Spatiotemporal Landscape of the Human Brain Epitranscriptome 07/01/2018 03/31/2023 03/31/2025 Not Reported Not Reported WEILL MEDICAL COLL OF CORNELL UNIV $3,311,487.00
U01MH116438-01 Massively parallel characterization of psychiatric disease associated regulatory elements in defined cell types 07/06/2018 03/31/2023 12/31/2023 Not Reported Not Reported UNIVERSITY OF CALIFORNIA, SAN FRANCISCO $3,339,852.00
U01MH116492-01 1/2 Discovery and validation of neuronal enhancers associated with the development of psychiatric disorders 07/06/2018 03/31/2023 03/31/2023 Not Reported Not Reported UNIV OF MASSACHUSETTS MED SCH WORCESTER $3,650,615.00
U01MH116488-01 1/2 Cell Type and Region-Specific Regulatory Networks in Human Brain Development and Disorders 07/06/2018 03/31/2023 03/31/2024 Not Reported Not Reported YALE UNIVERSITY $6,470,162.00
R01MH117293-01 1/3 Understanding PTSD through Postmortem Targeted Brain Multi-omics 07/25/2018 04/30/2023 02/28/2030 Not Reported Not Reported UNIVERSITY OF TEXAS AT AUSTIN $3,636,960.00
R01MH117292-01 Site 3/3, Understanding PTSD through Postmortem Targeted Brain Multiomics 07/25/2018 04/30/2023 02/28/2030 Not Reported Not Reported MCLEAN HOSPITAL $4,059,932.00
R01MH117291-01 2/3 Understanding PTSD through Postmortem Targeted Brain Multi-omics 07/25/2018 04/30/2023 02/28/2030 Not Reported Not Reported LIEBER INSTITUTE, INC. $4,418,548.00
R56MH114901-01 3/3 Chromatin regulation during brain development and in ASD 08/01/2018 07/31/2021 07/31/2021 Not Reported Not Reported DUKE UNIVERSITY $355,941.00
R56MH114899-01 2/3 Chromatin regulation during brain development and in ASD 08/01/2018 07/31/2020 07/31/2020 Not Reported Not Reported MAYO CLINIC ROCHESTER $129,927.00
U01MH116441-01 Dynamic RNA Modifications in human brain development and autism 08/01/2018 04/30/2023 04/30/2023 Not Reported Not Reported EMORY UNIVERSITY $4,939,503.00
R56MH114911-01 1/3 Chromatin regulation during brain development and in ASD 08/03/2018 07/31/2020 07/31/2020 Not Reported Not Reported YALE UNIVERSITY $550,583.00
U01MH116487-01 2/2 - Cell Type and Region-Specific Regulatory Networks in Human Brain Development and Disorders 08/15/2018 05/31/2023 05/31/2023 Not Reported Not Reported UNIVERSITY OF CALIFORNIA, SAN FRANCISCO $2,279,704.00
U01MH116489-01 2/2 Discovery and validation of neuronal enhancers associated with the development of psychiatric disorders 08/17/2018 04/30/2023 04/30/2025 Not Reported Not Reported UNIVERSITY OF CALIFORNIA LOS ANGELES $4,523,653.00
U01MH116442-01 The 3D genome in transcriptional regulation across the postnatal life span, with implications for schizophrenia and bipolar disorder 09/01/2018 05/31/2023 05/31/2024 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $5,895,770.00
U01DA048279-01 Functional genomic resource and integrative model of dopaminergic circuitry associated with psychiatric disease 05/01/2019 02/29/2024 02/29/2024 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $2,181,466.00
R01MH116529-01 Integrated, cell type specific functional genomics analyses of regulatory sequence elements and their dynamic interaction networks in neuropsychiatric brain tissues 06/20/2019 03/31/2024 03/31/2024 Not Reported Not Reported STANFORD UNIVERSITY $6,965,362.00
R01MH121521-01 Isoform-level probabilistic transcriptome-wide association to undercover neurogenetic mechanisms underlying complex psychiatric traits 01/03/2020 11/30/2024 11/30/2025 Not Reported Not Reported UNIVERSITY OF PENNSYLVANIA $3,367,214.00
U01MH122849-01 Spatial registration of gene expression in the human brain 05/01/2020 04/30/2022 04/30/2024 Not Reported Not Reported LIEBER INSTITUTE, INC. $1,747,260.00
U01MH122591-01 1/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease. 05/01/2020 02/28/2025 02/28/2026 Not Reported Not Reported UPSTATE MEDICAL UNIVERSITY $789,640.00
U01MH122592-01 3/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease 05/01/2020 02/28/2025 02/28/2025 Not Reported Not Reported UNIVERSITY OF CALIFORNIA, SAN DIEGO $656,659.00
U01MH122590-01 2/3 High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease 05/01/2020 02/28/2025 02/28/2027 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $2,180,793.00
U01MH122678-01 1/2 Identification and Validation of Expression Quantitative Trait Loci (eQTLs) in discrete cell types across human brain development 02/01/2021 11/30/2025 11/30/2025 Not Reported Not Reported YALE UNIVERSITY $3,639,826.00
U01MH122681-01 2/2 - Identification and Validation of Expression Quantitative Trait Loci (eQTLs) in discrete cell types across human brain development 02/10/2021 05/31/2026 05/31/2027 Not Reported Not Reported UNIVERSITY OF OXFORD $2,541,479.00
R01MH126393-01 Laminar dissection of cortical human brain gene expression in neuropsychiatric disorders 06/23/2021 03/31/2026 09/30/2026 Not Reported Not Reported LIEBER INSTITUTE, INC. $3,916,231.00
R01MH125516-01 Assessing Genomic, Regulatory and Transcriptional Variation at Single Nuclei Resolution in the Brains of Individuals with Autism Spectrum Disorder 07/27/2021 05/31/2026 05/31/2027 Not Reported Not Reported UNIVERSITY OF CALIFORNIA, SAN FRANCISCO $3,034,663.00
U01MH122509-01 Discovery and validation of genetic variation impacting the gene regulatory landscape during human cortical development 08/01/2021 04/30/2026 04/30/2026 Not Reported Not Reported UNIV OF NORTH CAROLINA CHAPEL HILL $2,806,641.00
R01MH126459-01 Gene Expression Regulation in Brains of East Asian, African, and European Descent Explains Schizophrenia GWAS in Diverse Populations. 03/25/2022 01/31/2027 01/31/2027 Not Reported Not Reported UPSTATE MEDICAL UNIVERSITY $3,694,152.00
R01MH129301-01 Sex-specific trajectories in epigenomic regulation of brain patterning 04/15/2022 01/31/2027 01/31/2027 Not Reported Not Reported YALE UNIVERSITY $4,545,530.00
R21MH129817-01 Mapping human brain cell type-specific isoform usage in ASD 05/11/2022 04/30/2024 07/31/2025 Not Reported Not Reported ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI $464,750.00

helpcenter.collection.general-tab

NDA Help Center

Collection - General Tab

Fields available for edit on the top portion of the page include:

  • Collection Title
  • Investigators
  • Collection Description
  • Collection Phase
  • Funding Source
  • Clinical Trials

Collection Phase: The current status of a research project submitting data to an NDA Collection, based on the timing of the award and/or the data that have been submitted.

  • Pre-Enrollment: The default entry made when the NDA Collection is created.
  • Enrolling: Data have been submitted to the NDA Collection or the NDA Data Expected initial submission date has been reached for at least one data structure category in the NDA Collection.
  • Data Analysis: Subject level data collection for the research project is completed and has been submitted to the NDA Collection. The NDA Collection owner or the NDA Help Desk may set this phase when they’ve confirmed data submission is complete and submitted subject counts match at least 90% of the target enrollment numbers in the NDA Data Expected. Data submission reminders will be turned off for the NDA Collection.
  • Funding Completed: The NIH grant award (or awards) associated with the NDA Collection has reached its end date. NDA Collections in Funding Completed phase are assigned a subphase to indicate the status of data submission.
    • The Data Expected Subphase indicates that NDA expects more data will be submitted
    • The Closeout Subphase indicates the data submission is complete.
    • The Sharing Not Met Subphase indicates that data submission was not completed as expected.

Blinded Clinical Trial Status:

  • This status is set by a Collection Owner and indicates the research project is a double blinded clinical trial. When selected, the public view of Data Expected will show the Data Expected items and the Submission Dates, but the targeted enrollment and subjects submitted counts will not be displayed.
  • Targeted enrollment and subjects submitted counts are visible only to NDA Administrators and to the NDA Collection or as the NDA Collection Owner.
  • When an NDA Collection that is flagged Blinded Clinical Trial reaches the maximum data sharing date for that Data Repository (see https://nda.nih.gov/nda/sharing-regimen.html), the embargo on Data Expected information is released.

Funding Source

The organization(s) responsible for providing the funding is listed here.

Supporting Documentation

Users with Submission privileges, as well as Collection Owners, Program Officers, and those with Administrator privileges, may upload and attach supporting documentation. By default, supporting documentation is shared to the general public, however, the option is also available to limit this information to qualified researchers only.

Grant Information

Identifiable details are displayed about the Project of which the Collection was derived from. You may click in the Project Number to view a full report of the Project captured by the NIH.

Clinical Trials

Any data that is collected to support or further the research of clinical studies will be available here. Collection Owners and those with Administrator privileges may add new clinical trials.

Frequently Asked Questions

  • How does the NIMH Data Archive (NDA) determine which Permission Group data are submitted into?
    During Collection creation, NDA staff determine the appropriate Permission Group based on the type of data to be submitted, the type of access that will be available to data access users, and the information provided by the Program Officer during grant award.
  • How do I know when a NDA Collection has been created?
    When a Collection is created by NDA staff, an email notification will automatically be sent to the PI(s) of the grant(s) associated with the Collection to notify them.
  • Is a single grant number ever associated with more than one Collection?
    The NDA system does not allow for a single grant to be associated with more than one Collection; therefore, a single grant will not be listed in the Grant Information section of a Collection for more than one Collection.
  • Why is there sometimes more than one grant included in a Collection?
    In general, each Collection is associated with only one grant; however, multiple grants may be associated if the grant has multiple competing segments for the same grant number or if multiple different grants are all working on the same project and it makes sense to hold the data in one Collection (e.g., Cooperative Agreements).

Glossary

  • Administrator Privilege
    A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users.
  • Collection Owner
    Generally, the Collection Owner is the contact PI listed on a grant. Only one NDA user is listed as the Collection owner. Most automated emails are primarily sent to the Collection Owner.
  • Collection Phase
    The Collection Phase provides information on data submission as opposed to grant/project completion so while the Collection phase and grant/project phase may be closely related they are often different. Collection users with Administrative Privileges are encouraged to edit the Collection Phase. The Program Officer as listed in eRA (for NIH funded grants) may also edit this field. Changes must be saved by clicking the Save button at the bottom of the page. This field is sortable alphabetically in ascending or descending order. Collection Phase options include:
    • Pre-Enrollment: A grant/project has started, but has not yet enrolled subjects.
    • Enrolling: A grant/project has begun enrolling subjects. Data submission is likely ongoing at this point.
    • Data Analysis: A grant/project has completed enrolling subjects and has completed all data submissions.
    • Funding Completed: A grant/project has reached the project end date.
  • Collection Title
    An editable field with the title of the Collection, which is often the title of the grant associated with the Collection.
  • Grant
    Provides the grant number(s) for the grant(s) associated with the Collection. The field is a hyperlink so clicking on the Grant number will direct the user to the grant information in the NIH Research Portfolio Online Reporting Tools (RePORT) page.
  • Supporting Documentation
    Various documents and materials to enable efficient use of the data by investigators unfamiliar with the project and may include the research protocol, questionnaires, and study manuals.
  • NIH Research Initiative
    NDA Collections may be organized by scientific similarity into NIH Research Initiatives, to facilitate query tool user experience. NIH Research Initiatives map to one or multiple Funding Opportunity Announcements.
  • Permission Group
    Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.
  • Planned Enrollment
    Number of human subject participants to be enrolled in an NIH-funded clinical research study. The data is provided in competing applications and annual progress reports.
  • Actual Enrollment
    Number of human subjects enrolled in an NIH-funded clinical research study. The data is provided in annual progress reports.
  • NDA Collection
    A virtual container and organization structure for data and associated documentation from one grant or one large project/consortium. It contains tools for tracking data submission and allows investigators to define a wide array of other elements that provide context for the data, including all general information regarding the data and source project, experimental parameters used to collect any event-based data contained in the Collection, methods, and other supporting documentation. They also allow investigators to link underlying data to an NDA Study, defining populations and subpopulations specific to research aims.
  • Data Use Limitations
    Data Use Limitations (DULs) describe the appropriate secondary use of a dataset and are based on the original informed consent of a research participant. NDA only accepts consent-based data use limitations defined by the NIH Office of Science Policy.
  • Total Subjects Shared
    The total number of unique subjects for whom data have been shared and are available for users with permission to access data.
IDNameCreated DateStatusType
2498Test Experiment: Please Disregard03/04/2024ApprovedOmics
2501ATACSeq_MouseHAL03/05/2024ApprovedOmics
2502rnaSeq_NHP-Chimpanzee03/05/2024ApprovedOmics
2503rnaSeq_NHP-Macaque03/05/2024ApprovedOmics
25043Dchromatin_HI-C03/06/2024ApprovedOmics
2505rnaSeq_BipSeq03/06/2024ApprovedOmics
2506ATACSeq_BrainDev3D03/06/2024ApprovedOmics
2507rnaSeq_BrainDev3D03/06/2024ApprovedOmics
2508HI-C_BrainDev3D03/06/2024ApprovedOmics
2509ChIPSeq_BrainDev3D03/06/2024ApprovedOmics
2510ATACSeq_BrainGVEX03/06/2024ApprovedOmics
2511rnaSeq_BrainGVEX03/06/2024ApprovedOmics
2512RPPA_BrainGVEX03/06/2024ApprovedOmics
2513TMT_BrainGVEX03/06/2024ApprovedOmics
2514miRNASeq_BrainGVEX03/06/2024ApprovedOmics
2515WGS_BrainGVEX03/06/2024ApprovedOmics
2516rnaSeq_BrainSpan03/06/2024ApprovedOmics
2517ChIPSeq_BrainTF_203/06/2024ApprovedOmics
2518ATACSeq_BrainTF03/06/2024ApprovedOmics
2519Methylation_BrainTF03/06/2024ApprovedOmics
2520rnaSeq_BrainTF03/06/2024ApprovedOmics
2521WGS_BrainTF03/06/2024ApprovedOmics
2522rnaSeq_BrainVar03/06/2024ApprovedOmics
2523WGS_BrainVar03/06/2024ApprovedOmics
2524rnaSeq_CMC03/06/2024ApprovedOmics
2525scrnaSeq_CMC03/06/2024ApprovedOmics
2526ChIPSeq_CNON03/06/2024ApprovedOmics
2527HI-C_CNON03/06/2024ApprovedOmics
2528NOMeseq_CNON03/06/2024ApprovedOmics
2529HI-C_DopaModel03/06/2024ApprovedOmics
2530rnaSeq_DopaModel03/06/2024ApprovedOmics
2531ChIPSeq_EpiDiff03/06/2024ApprovedOmics
2532ChIPSeq_EpiDiff-II03/06/2024ApprovedOmics
2533Bisulfite-Seq_EpiGABA03/06/2024ApprovedOmics
2534ChIPSeq_EpiGABA03/06/2024ApprovedOmics
2535ERRBS_EpiGABA03/06/2024ApprovedOmics
2536Methylation_EpiGABA03/06/2024ApprovedOmics
2537rnaSeq_EpiGABA03/06/2024ApprovedOmics
2538ChIPSeq_EpiMap03/06/2024ApprovedOmics
2539ATACSeq_HumanFC03/06/2024ApprovedOmics
2540Bisulfite-Seq_LIBD-WGBS03/06/2024ApprovedOmics
2541Bisulfite-Seq_LIBD-WGBS-SCZD03/06/2024ApprovedOmics
2542HI-C_MidbrainGenomics03/06/2024ApprovedOmics
2543Bisulfite-Seq_NeuMet03/06/2024ApprovedOmics
2544oxBSseq_NeuMet03/06/2024ApprovedOmics
2545ATACSeq_NeuREs03/06/2024ApprovedOmics
2546CUTTag_NeuREs03/06/2024ApprovedOmics
2547ChIPSeq_NeuREs03/06/2024ApprovedOmics
2548rnaSeq_NeuREs03/06/2024ApprovedOmics
2549scrnaSeq_NeuREs03/06/2024ApprovedOmics
2550scrnaSeq_SZBDMulti-Seq03/06/2024ApprovedOmics
2551rnaSeq_SingleCellRNAseq03/06/2024ApprovedOmics
2552ChIPSeq_UCLA-ASD03/06/2024ApprovedOmics
2553Methylation_UCLA-ASD03/06/2024ApprovedOmics
2554rnaSeq_UCLA-ASD03/06/2024ApprovedOmics
2555bulkrnaSeq_UCLA-ASD03/06/2024ApprovedOmics
2556mirnaSeq_UCLA-ASD03/06/2024ApprovedOmics
2557scATACSeq_UCLA-ASD03/06/2024ApprovedOmics
2558scrnaSeq_UCLA-ASD03/06/2024ApprovedOmics
2559WGBS_WGBS-Pilot03/06/2024ApprovedOmics
2560ChIPSeq_Yale-ASD03/06/2024ApprovedOmics
2561rnaSeq_Yale-ASD03/06/2024ApprovedOmics
2562WGBS_flowRNA-WGBS03/06/2024ApprovedOmics
2563ATACSeq_iPSC03/06/2024ApprovedOmics
2564ChIPSeq_iPSC03/06/2024ApprovedOmics
2565rnaSeq_iPSC03/06/2024ApprovedOmics
2566scrnaSeq_iPSC03/06/2024ApprovedOmics
2567ATACSeq_iPSC-ASD03/06/2024ApprovedOmics
2568HI-C_iPSC-HiC03/07/2024ApprovedOmics
2569Proteomics_iPSCNeuroDiff03/07/2024ApprovedOmics
2570rnaSeq_iPSCNeuroDiff03/07/2024ApprovedOmics
2571isoSeq_lncRNA-Pilot03/07/2024ApprovedOmics
2572rnaSeq_lncRNA-Pilot03/07/2024ApprovedOmics
2573ATACSeq_referenceBrain03/07/2024ApprovedOmics
2574Bisulfite-Seq_referenceBrain03/07/2024ApprovedOmics
2575ChIPSeq_referenceBrain03/07/2024ApprovedOmics
2576HI-C_referenceBrain03/07/2024ApprovedOmics
2578isoSeq_referenceBrain03/07/2024ApprovedOmics
2579rnaSeq_referenceBrain03/07/2024ApprovedOmics
2580RPPA_referenceBrain03/07/2024ApprovedOmics
2581ATACSeq_CMC_Controlled03/07/2024ApprovedOmics
2582ATACSeq_CMC_Open03/07/2024ApprovedOmics
2583snpArray_BipSeq03/14/2024ApprovedOmics
2584snpArray_LIBD-WGBS03/14/2024ApprovedOmics
2585RNASeq_CMC_Controlled03/14/2024ApprovedOmics
2586RNASeq_CMC_Open03/14/2024ApprovedOmics
2588SNP_CMC_Controlled03/15/2024ApprovedOmics
2589WGS_CMS_Controlled03/15/2024ApprovedOmics
2591WGS_LIBD-WGBS-SCZD03/21/2024ApprovedOmics
2593ChIPSeq_Capstone03/25/2024ApprovedOmics
2594RNASeq_Capstone03/25/2024ApprovedOmics
2595WGS_Capstone03/25/2024ApprovedOmics
2596RNASeq_PsychiPSCneurons03/25/2024ApprovedOmics
2797snpArray_EpiGABA01/06/2025ApprovedOmics
2799ATACSeq_BrainGVEX01/06/2025ApprovedOmics
2800ATACSeq_CMC01/06/2025ApprovedOmics
2801ATACSeq_HumanFC01/07/2025ApprovedOmics
2802Bisulfite-Seq_EpiGABA01/07/2025ApprovedOmics
2859Bisulfite-Seq_flowRNA_WGBS02/17/2025ApprovedOmics
2860EM-seq_BrainTF02/17/2025ApprovedOmics
2871ChIPSeq_BrainTF02/24/2025ApprovedOmics
2872CITESeq_snMultiRegionDevelopmentalTranscriptomics02/24/2025ApprovedOmics
2873HiChIPseq_iPSC-ASD02/24/2025ApprovedOmics
2874lentiMPRA_NeuREs02/24/2025ApprovedOmics
2875lncrnaSeq_ASD-lncRNA02/24/2025ApprovedOmics
2876long-read-rnaSeq_MultiomeBrain02/24/2025ApprovedOmics
2877long-read-rnaSeq_UCLA-DevCtx02/24/2025ApprovedOmics
2878m6A-rnaSeq_m6A-seqAutism02/24/2025ApprovedOmics
2879oxBS-Seq_EpiGABA02/24/2025ApprovedOmics
2880Ribo-Seq_BrainGVEX02/24/2025ApprovedOmics
2881rnaSeq_CMC_HBCC02/25/2025ApprovedOmics
2882rnaSeq_EpiMap02/25/2025ApprovedOmics
2883rnaSeq_LIBD_szControl02/25/2025ApprovedOmics
2884rnaSeq_MDDseq02/25/2025ApprovedOmics
2885scATACseq_MultiomeBrain02/25/2025ApprovedOmics
2886snRNAseq_DevBrain03/03/2025ApprovedOmics
2887scRNAseq_IsoHuB03/03/2025ApprovedOmics
2888scRNAseq_LIBD_U01_DLPFC03/03/2025ApprovedOmics
2889scRNAseq_MultiomeBrain03/03/2025ApprovedOmics
2890scRNAseq_PTSDBrainomics03/03/2025ApprovedOmics
2891scRNAseq_scOrganomics03/03/2025ApprovedOmics
2892scRNAseq_SingleCellRNAseq03/03/2025ApprovedOmics
2893snpArray_BrainGVEX03/03/2025ApprovedOmics
2894snpArray_BrainSpan03/03/2025ApprovedOmics
2895snpArray_IsoHuB03/03/2025ApprovedOmics
2896snpArray_LIBD_U01_DLPFC03/03/2025ApprovedOmics
2897snpArray_MDDseq03/03/2025ApprovedOmics
2898imputedGenotypes_brainSCOPE03/03/2025ApprovedOmics
2899snpArray_PTSDBrainomics03/03/2025ApprovedOmics
2900snpArray_SZBDMulti-Seq03/03/2025ApprovedOmics
2901snpArray_UCLA-ASD03/03/2025ApprovedOmics
2902STARRSeq_NeuEnhancer03/03/2025ApprovedOmics
2903WGS_MultiomeBrain03/03/2025ApprovedOmics
2904MPRA_iPSC-ASD03/03/2025ApprovedOmics
2938Archive04/29/2025ApprovedOmics
helpcenter.collection.experiments-tab

NDA Help Center

Collection - Experiments

The number of Experiments included is displayed in parentheses next to the tab name. You may download all experiments associated with the Collection via the Download button. You may view individual experiments by clicking the Experiment Name and add them to the Filter Cart via the Add to Cart button.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may create or edit an Experiment.

Please note: The creation of an NDA Experiment does not necessarily mean that data collected, according to the defined Experiment, has been submitted or shared.

Frequently Asked Questions

  • Can an Experiment be associated with more than one Collection?

    Yes -see the “Copy” button in the bottom left when viewing an experiment. There are two actions that can be performed via this button:

    1. Copy the experiment with intent for modifications.
    2. Associate the experiment to the collection. No modifications can be made to the experiment.

Glossary

  • Experiment Status
    An Experiment must be Approved before data using the associated Experiment_ID may be uploaded.
  • Experiment ID
    The ID number automatically generated by NDA which must be included in the appropriate file when uploading data to link the Experiment Definition to the subject record.
ATAC Sequencing Genomics 3015
Bisulfite Sequencing Genomics 137
ChIP Sequencing Genomics 706
High-throughput Chromosome Conformation Capture (Hi-C) Genomics 110
Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) Genomics 65
Proteomics Samples Genomics 666
PsychENCODE/Common Mind Summary Clinical Assessments 1884
RNA Sequencing Genomics 2875
SNP Array Genomics 1631
Whole Genome Sequencing Genomics 658
helpcenter.collection.shared-data-tab

NDA Help Center

Collection - Shared Data

This tab provides a quick overview of the Data Structure title, Data Type, and Number of Subjects that are currently Shared for the Collection. The information presented in this tab is automatically generated by NDA and cannot be edited. If no information is visible on this tab, this would indicate the Collection does not have shared data or the data is private.

The shared data is available to other researchers who have permission to access data in the Collection's designated Permission Group(s). Use the Download button to get all shared data from the Collection to the Filter Cart.

Frequently Asked Questions

  • How will I know if another researcher uses data that I shared through the NIMH Data Archive (NDA)?
    To see what data your project have submitted are being used by a study, simply go the Associated Studies tab of your collection. Alternatively, you may review an NDA Study Attribution Report available on the General tab.
  • Can I get a supplement to share data from a completed research project?
    Often it becomes more difficult to organize and format data electronically after the project has been completed and the information needed to create a GUID may not be available; however, you may still contact a program staff member at the appropriate funding institution for more information.
  • Can I get a supplement to share data from a research project that is still ongoing?
    Unlike completed projects where researchers may not have the information needed to create a GUID and/or where the effort needed to organize and format data becomes prohibitive, ongoing projects have more of an opportunity to overcome these challenges. Please contact a program staff member at the appropriate funding institution for more information.

Glossary

  • Data Structure
    A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure
  • Data Type
    A grouping of data by similar characteristics such as Clinical Assessments, Omics, or Neurosignal data.
  • Shared
    The term 'Shared' generally means available to others; however, there are some slightly different meanings based on what is Shared. A Shared NDA Study is viewable and searchable publicly regardless of the user's role or whether the user has an NDA account. A Shared NDA Study does not necessarily mean that data used in the NDA Study have been shared as this is independently determined. Data are shared according the schedule defined in a Collection's Data Expected Tab and/or in accordance with data sharing expectations in the NDA Data Sharing Terms and Conditions. Additionally, Supporting Documentation uploaded to a Collection may be shared independent of whether data are shared.

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Publications

Publications relevant to NDA data are listed below. Most displayed publications have been associated with the grant within Pubmed. Use the "+ New Publication" button to add new publications. Publications relevant/not relevant to data expected are categorized. Relevant publications are then linked to the underlying data by selecting the Create Study link. Study provides the ability to define cohorts, assign subjects, define outcome measures and lists the study type, data analysis and results. Analyzed data and results are expected in this way.

PubMed IDStudyTitleJournalAuthorsDateStatus
42026031Create StudyAugmenting extinction with counterconditioning strengthens and sustains neural safety representations in PTSD.Translational psychiatryCooper, Samuel E; Keller, Nicole E; Bauer, Elizabeth A; Lambert, Sydney R; Hennings, Augustin C; Azar, Ameera A; Bibb, Sophia A; Nemeroff, Charles B; Cisler, Josh M; Lewis-Peacock, Jarrod A; Dunsmoor, Joseph EApril 23, 2026Not Determined
41875888Create StudyPan-neurodegeneration proteomics reveals disease subtypes and molecular signatures.CellShrestha, Him K; Sun, Huan; Yarbro, Jay M; Lee, DongGeun; Liu, Danting; Wang, Erming; McReynolds, Meghan; Zhang, Nan; Xie, Boer; Yang, Shu; Yu, Kaiwen; Poudel, Suresh; Li, Yuxin; Yuan, Zuo-Fei; Kong, Dehui; Wang, Minghui; Wang, Zhen; Niu, Mingming; Wang, Hong; Zaman, Masihuz; Wang, Ju; Vanderwall, David R; Sun, Yu; Wu, Zhiping; Chen, Ping-Chung; Bai, Bing; High, Anthony A; Faura, Júlia; Liu, Chunyu; Bennett, David A; Johnson, Erik C B; Seyfried, Nicholas T; Levey, Allan I; Haroutunian, Vahram; Serrano, Geidy E; Beach, Thomas G; DeTure, Michael; Kanekiyo, Takahisa; Petersen, Ronald C; Bu, Guojun; McLean, Pamela J; Dickson, Dennis W; Rademakers, Rosa; Yu, Gang; Wang, Xusheng; Zhang, Bin; Peng, JunminMarch 23, 2026Not Determined
41831411Create StudyIntegrating multiomic layers to decode psychiatric disease mechanisms.Current opinion in genetics & developmentSheu, Lyra; Girdhar, Kiran; Roussos, PanosMarch 13, 2026Not Determined
41757081Create StudyMapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex.bioRxiv : the preprint server for biologyKwon, Sang Ho; Guo, Boyi; Fang, Cindy; Tippani, Madhavi; Bach, Svitlana V; Miller, Ryan A; Maguire, Sarah E; Iatrou, Artemis; Pertea, Geo; Eagles, Nicholas J; Valentine, Madeline R; Oh, Seyun; Jajoo, Aarti; Balakundi, Vijetha; Du, Yufeng; Nguyen, Annie B; Zhang, Ruth; Kaipa, Uma M; Divecha, Heena R; Lobana, Jashandeep S; Kleinman, Joel E; Han, Shizhong; Daskalakis, Nikolaos P; Hyde, Thomas M; Collado-Torres, Leonardo; Page, Stephanie C; Maynard, Kristen R; Hicks, Stephanie C; Martinowich, KeriFebruary 16, 2026Not Determined
41639050Create StudySeveral novel classes of small regulatory RNAs show widespread changes in schizophrenia and bipolar disorder and extensive linkages to critical brain processes.Translational psychiatryNersisyan, Stepan; Loher, Phillipe; Nazeraj, Iliza; Shao, Zhiping; Fullard, John F; Voloudakis, Georgios; Girdhar, Kiran; Roussos, Panos; Rigoutsos, IsidoreFebruary 4, 2026Not Determined
41611887Create StudyDevelopmental convergence and divergence in human stem cell models of autism.NatureGordon, Aaron; Yoon, Se-Jin; Bicks, Lucy K; Martín, Jacqueline M; Pintacuda, Greta; Arteaga, Stephanie; Wamsley, Brie; Guo, Qiuyu; Elahi, Lubayna; Dolmetsch, Ricardo E; Bernstein, Jonathan A; O'Hara, Ruth; Hallmayer, Joachim F; Lage, Kasper; Pasca, Sergiu P; Geschwind, Daniel HMarch 1, 2026Not Determined
41394650Create StudyHigh cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood.bioRxiv : the preprint server for biologyVochteloo, Martijn; Kooijmans, Anoek; Bakker, Joost; Oelen, Roy; Niewold, Jelmer; Kaptijn, Dan; Bonder, Marc Jan; van der Wijst, Monique; Huang, Yunfeng; Bryois, Julien; Tsai, Ellen A; Franke, Lude; Westra, Harm-JanNovember 28, 2025Not Determined
41372416Create StudyMapping the genetic landscape across 14 psychiatric disorders.NatureGrotzinger, Andrew D; Werme, Josefin; Peyrot, Wouter J; Frei, Oleksandr; de Leeuw, Christiaan; Bicks, Lucy K; Guo, Qiuyu; Margolis, Michael P; Coombes, Brandon J; Batzler, Anthony; Pazdernik, Vanessa; Biernacka, Joanna M; Andreassen, Ole A; Anttila, Verneri; Børglum, Anders D; Breen, Gerome; Cai, Na; Demontis, Ditte; Edenberg, Howard J; Faraone, Stephen V; Franke, Barbara; Gandal, Michael J; Gelernter, Joel; Hatoum, Alexander S; Hettema, John M; Johnson, Emma C; Jonas, Katherine G; Knowles, James A; Koenen, Karestan C; Maihofer, Adam X; Mallard, Travis T; Mattheisen, Manuel; Mitchell, Karen S; Neale, Benjamin M; Nievergelt, Caroline M; Nurnberger, John I; O'Connell, Kevin S; Peterson, Roseann E; Robinson, Elise B; Sanchez-Roige, Sandra S; Santangelo, Susan L; Scharf, Jeremiah M; Stefansson, Hreinn; Stefansson, Kari; Stein, Murray B; Strom, Nora I; Thornton, Laura M; Tucker-Drob, Elliot M; Verhulst, Brad; Waldman, Irwin D; Walters, G Bragi; Wray, Naomi R; Yu, Dongmei; Anxiety Disorders Working Group of the Psychiatric Genomics Consortium; Attention-Deficit/Hyperactivity Disorder (ADHD) Working Group of the Psychiatric Genomics Consortium; Autism Spectrum Disorders Working Group of the Psychiatric Genomics Consortium; Bipolar Disorder Working Group of the Psychiatric Genomics Consortium; Eating Disorders Working Group of the Psychiatric Genomics Consortium; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium; Nicotine Dependence GenOmics (iNDiGO) Consortium; Obsessive-Compulsive Disorder and Tourette Syndrome Working Group of the Psychiatric Genomics Consortium; Post-Traumatic Stress Disorder Working Group of the Psychiatric Genomics Consortium; Schizophrenia Working Group of the Psychiatric Genomics Consortium; Substance Use Disorders Working Group of the Psychiatric Genomics Consortium; Lee, Phil H; Kendler, Kenneth S; Smoller, Jordan WJanuary 1, 2026Not Determined
41366183Create StudyMulti-region m6A epitranscriptome profiling of the human brain reveals spatial and temporal variation and enrichment of disease-associated loci.Nature neuroscienceShafik, Andrew M; Peng, Yong; Zhang, Zijie; Chang, Chen; Wang, Pingluan; Lim, Junghwa; Song, Hongjun; He, Chuan; Chen, Mengjie; Jin, PengJanuary 1, 2026Not Determined
41356351Create StudyDopamine receptor 1-expressing cells in the ventral hippocampus encode cocaine-context associations.Research squareKondev, Veronika; Godino, Arthur; Kipp, Brian T; Hennigan, Evelyn; Casey, Clara; Patel, Vishwendra; Naguib, Sarah; Ripp, Adam; Abroon, Jacob; Kahn, Liz; Racine, Isla; Chen, Earnest P; Blaschke, Clementine; Minier-Toribio, Angelica; Estill, Molly; LaBanca, Alexa; Gan, Li; Fullard, John F; Roussos, Panos; Nestler, Eric JNovember 25, 2025Not Determined
41332620Create StudyOrchestrating Spatial Transcriptomics Analysis with Bioconductor.bioRxiv : the preprint server for biologyCrowell, Helena L; Dong, Yixing; Billato, Ilaria; Cai, Peiying; Emons, Martin; Gunz, Samuel; Guo, Boyi; Li, Mengbo; Mahmoud, Alexandru; Manukyan, Artür; Pagès, Hervé; Panwar, Pratibha; Rao, Shreya; Sargeant, Callum J; Kern, Lori Shepherd; Ramos, Marcel; Sun, Jieran; Totty, Michael; Carey, Vincent J; Chen, Yunshun; Collado-Torres, Leonardo; Ghazanfar, Shila; Hansen, Kasper D; Martinowich, Keri; Maynard, Kristen R; Patrick, Ellis; Righelli, Dario; Risso, Davide; Tiberi, Simone; Waldron, Levi; Gottardo, Raphael; Robinson, Mark D; Hicks, Stephanie C; Weber, Lukas MNovember 21, 2025Not Determined
41315269Create StudyImpact of common variants on brain gene expression from RNA to protein to schizophrenia risk.Nature communicationsLiang, Qiuman; Jiang, Yi; Shieh, Annie W; Zhou, Dan; Chen, Rui; Wang, Feiran; Xu, Meng; Niu, Mingming; Wang, Xusheng; Pinto, Dalila; Wang, Yue; Cheng, Lijun; Vadukapuram, Ramu; Zhang, Chunling; Grennan, Kay; Giase, Gina; White, Kevin P; Peng, Junmin; Li, Bingshan; Liu, Chunyu; Chen, Chao; Wang, Sidney HNovember 28, 2025Not Determined
41293024Create StudyCell-type-resolved NRXN1 isoforms across human brain tissues and hiPSC organoids.bioRxiv : the preprint server for biologyCao, Lei; Fan, Yu; Ghorbani, Sadaf; Mariani, Jessica; Zhang, Yanchun; Fernando, Michael B; Bendl, Jaroslav; Fullard, John; Ramos, Susana Isabel; Mead, Edward A; Deikus, Gintaras; Beaumont, Kristin G; Sebra, Robert; Tsankova, Nadejda; Roussos, Panos; Brennand, Kristen J; Fang, GangNovember 11, 2025Not Determined
41279957Create StudyComputational modelling of schizophrenia-associated alterations of ion-channel-encoding gene expression predicts a decrease in delta power.bioRxiv : the preprint server for biologyKismul, Jan Fredrik; Ness, Torbjørn V; Elvsåshagen, Torbjørn; Andreassen, Ole; Einevoll, Gaute T; Linne, Marja-Leena; Mäki-Marttunen, TuomoOctober 20, 2025Not Determined
41279531Create StudyA spatial transcriptomic atlas of autism-associated genes identifies convergence in the developing human thalamus.bioRxiv : the preprint server for biologyAivazidis, Alexander; Memi, Fani; Rademaker, Koen; Koko, Mahmoud; Roberts, Kenny; Trinh, Andrew; Petryszak, Robert; Kleshchevnikov, Vitalii; Tuck, Liz; Lisgo, Steven; Li, Tong; Makarchuk, Stanislaw; Prete, Martin; Nowakowski, Tomasz J; Martin, Hilary C; Bayraktar, Omer AliNovember 6, 2025Not Determined
41279076Create StudyDisruption of Cell-Type-Specific Molecular Programs of Medium Spiny Neurons in Autism.bioRxiv : the preprint server for biologyYuan, Guohua; Suresh, Varun; Wigdor, Emilie; Hao, Yuhan; Leonard, Rachel; Steyert, Marilyn; Griffiths, Michael; Evans, Clements; Rohani, Narjes; Weiss, Jakob; Lassen, Frederik H; Schafer, Nicole; Dong, Shan; Palmer, Duncan S; Sanders, Stephan J; Nowakowski, Tomasz JNovember 7, 2025Not Determined
41278953Create StudyLarge-scale discovery of neural enhancers for cis-regulation therapies.bioRxiv : the preprint server for biologyMcDiarmid, Troy A; Page, Nicholas F; Chardon, Florence M; Daza, Riza M; Chen, George T; Kosicki, Michael; James, Lucas M; Nourie, Hannah C; Laboy-Cintrón, Dianne; Lee, Arthur S; Vij, Paula; Calderon, Diego; Lalanne, Jean-Benoît; Martin, Beth K; Fink, Kyle; Talkowski, Michael E; Muotri, Alysson R; Philpot, Benjamin D; Pennacchio, Len A; Geschwind, Daniel H; Sanders, Stephan J; Ahituv, Nadav; Shendure, JayNovember 5, 2025Not Determined
41256666Create StudyComputational modelling of novelty detection in the mismatch negativity protocols and its impairments in schizophrenia.bioRxiv : the preprint server for biologyEissa, Ahmed; Kismul, Jan Fredrik; Pentz, Atle Bråthen; Elvsåshagen, Torbjorn; Metzner, Christoph; Akkouh, Ibrahim; Djurovic, Srdjan; Shadrin, Alexey; Linne, Marja-Leena; Einevoll, Gaute T; Andreassen, Ole A; Mäki-Marttunen, TuomoOctober 1, 2025Not Determined
41197609Create StudyFrom variants to mechanisms: Neurogenomics in the post-GWAS era.NeuronMargolis, Michael P; Tang, Miao; Gagliardi, Miriam; Wen, Cindy; Wu, Yeda; Wray, Naomi R; Ziller, Michael J; Gandal, Michael JNovember 5, 2025Not Determined
41187489Create StudyUnique and divergent features of human brain development.Current opinion in neurobiologySalamon, Iva; Doyle, Daniel Z; Bandler, Rachel C; Pattabiraman, Kartik; Sestan, NenadDecember 1, 2025Not Determined
41145887Create StudyThe neuronal chromatin landscape in brains from individuals with schizophrenia is linked to early fetal development.Nature neuroscienceGirdhar, Kiran; Bendl, Jaroslav; Baumgartner, Andrew; Therrien, Karen; Venkatesh, Sanan; Bercovitch, Rachel; Mathur, Deepika; Dong, Pengfei; Rahman, Samir; Kleopoulos, Steven P; Misir, Ruth; Reach, Sarah M; Auluck, Pavan K; Marenco, Stefano; Lewis, David A; Haroutunian, Vahram; Funk, Cory C; Voloudakis, Georgios; Hoffman, Gabriel E; Fullard, John F; Roussos, PanosDecember 1, 2025Not Determined
41120370Create StudyNeuroimaging transcriptomic analyses of Parkinson''s disease highlight molecular, cellular, and neurobiological mechanisms.NPJ Parkinson''s diseaseBledsoe, Xavier; Betti, Michael J; Gamazon, Eric ROctober 21, 2025Not Determined
41087377Create StudyGenomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station.Scientific reportsKarouia, Fathi; de Oliveira, Lorraine Christine; Hameed, Asif; Simpson, Anna; Singh, Nitin; Rekha, Punchappady D; Mason, Christopher E; Venkateswaran, KasthuriOctober 14, 2025Not Determined
41072639Create StudySex Differences in Brain Cell Type-Specific Chromatin Accessibility in Schizophrenia.Biological psychiatryMa, Yixuan; Girdhar, Kiran; Hoffman, Gabriel E; Fullard, John F; Bendl, Jaroslav; Roussos, PanosApril 1, 2026Not Determined
40964325Create StudyHuman-specific features of the cerebellum and ZP2-regulated synapse development.bioRxiv : the preprint server for biologyKim, Suel-Kee; Cherskov, Adriana; Sindhwani, Aastha; Choi, Sang-Hun; Kim, Hyojin; Li, Ming-Li; Zhang, Menglei; Mato-Blanco, Xoel; Liu, Yuting; Micali, Nicola; Young, David M; Estacion, Mark; Zhang, Yueqi; Ruiz-Jiménez, José Manuel; Nadkarni, Anandita; Luria, Victor; Sindhu, Suvimal Kumar; Chatterjee, Ipsita; Shibata, Akemi; Liang, Dan; Cho, Hyesun; Park, Saejeong; Spajic, Ana; Kovner, Rothem; Glavan, Martina; Chen, Rachel J; Risgaard, Ryan D; Li, Xinyun; Pochareddy, Sirisha; Karger, Amir; Huttner, Anita; Morozov, Yury M; Daadi, Etienne W; Colantuoni, Carlo; Gobeske, Kevin T; Ely, John J; Hof, Patrick R; Daadi, Marcel M; Sherwood, Chet C; Duque, Alvaro; Ma, Shaojie; Sousa, Andre M M; Waxman, Stephen G; Rakic, Pasko; Santpere, Gabriel; Sanders, Stephan J; Sestan, NenadSeptember 9, 2025Not Determined
helpcenter.collection.publications-tab

NDA Help Center

Collection - Publications

The number of Publications is displayed in parentheses next to the tab name. Clicking on any of the Publication Titles will open the Publication in a new internet browsing tab.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may mark a publication as either Relevant or Not Relevant in the Status column.

Frequently Asked Questions

  • How can I determine if a publication is relevant?
    Publications are considered relevant to a collection when the data shared is directly related to the project or collection.
  • Where does the NDA get the publications?
    PubMed, an online library containing journals, articles, and medical research. Sponsored by NiH and National Library of Medicine (NLM).

Glossary

  • Create Study
    A link to the Create an NDA Study page that can be clicked to start creating an NDA Study with information such as the title, journal and authors automatically populated.
  • Not Determined Publication
    Indicates that the publication has not yet been reviewed and/or marked as Relevant or Not Relevant so it has not been determined whether an NDA Study is expected.
  • Not Relevant Publication
    A publication that is not based on data related to the aims of the grant/project associated with the Collection or not based on any data such as a review article and, therefore, an NDA Study is not expected to be created.
  • PubMed
    PubMed provides citation information for biomedical and life sciences publications and is managed by the U.S. National Institutes of Health's National Library of Medicine.
  • PubMed ID
    The PUBMed ID is the unique ID number for the publication as recorded in the PubMed database.
  • Relevant Publication
    A publication that is based on data related to the aims of the grant/project associated with the Collection and, therefore, an NDA Study is expected to be created.
Data Expected List: Mandatory Data Structures

These data structures are mandatory for your NDA Collection. Please update the Targeted Enrollment number to accurately represent the number of subjects you expect to submit for the entire study.

For NIMH HIV-related research that involves human research participants: Select the dictionary or dictionaries most appropriate for your research. If your research does not require all three data dictionaries, just ignore the ones you do not need. There is no need to delete extra data dictionaries from your NDA Collection. You can adjust the Targeted Enrollment column in the Data Expected tab to “0” for those unnecessary data dictionaries. At least one of the three data dictionaries must have a non-zero value.

Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
Genomics/omics info icon
3,20003/14/2024
0
Approved
Research Subject and Pedigree info icon
101/15/2019
0
Approved
NIH Data Use Limitations info icon
3,20003/14/2024
0
Approved
To create your project's Data Expected list, use the "+New Data Expected" to add or request existing structures and to request new Data Structures that are not in the NDA Data Dictionary.

If the Structure you need already exists, locate it and specify your dates and enrollment when adding it to your Data Expected list. If you require changes to the Structure you need, select the indicator stating "No, it requires changes to meet research needs," and upload a file containing your requested changes.

If the structure you need is not yet defined in the Data Dictionary, you can select "Upload Definition" and attach the necessary materials to request its creation.

When selecting the expected dates for your data, make sure to follow the standard Data Sharing Regimen and choose dates within the date ranges that correspond to your project start and end dates.

Please visit the Completing Your Data Expected Tutorial for more information.
Data Expected List: Data Structures per Research Aims

These data structures are specific to your research aims and should list all data structures in which data will be collected and submitted for this NDA Collection. Please update the Targeted Enrollment number to accurately represent the number of subjects you expect to submit for the entire study.

Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
Summary info icon
3,20003/18/2024
0
Approved
Hi-C info icon
3,20003/14/2024
110
Approved
Bisulfite Sequencing info icon
3,20003/14/2024
137
Approved
ChIP Sequencing info icon
3,20003/14/2024
706
Approved
SNP Array info icon
3,20003/14/2024
1,631
Approved
RNA Sequencing info icon
3,20003/14/2024
2,875
Approved
Whole Genome Sequencing info icon
3,20003/14/2024
658
Approved
ATAC Sequencing info icon
3,20003/08/2024
3,015
Approved
Proteomics samples info icon
3,20003/14/2024
666
Approved
PsychENCODE/Common Mind Summary info icon
3,20003/18/2024
1,884
Approved
Nucleosome Occupancy and Methylome Sequencing info icon
3,20003/14/2024
65
Approved
PsychENCODE NOMe Sequencing info icon
10003/13/2024
0
Requested New
Structure not yet defined
No Status history for this Data Expected has been recorded yet
helpcenter.collection.data-expected-tab

NDA Help Center

Collection - Data Expected

The Data Expected tab displays the list of all data that NDA expects to receive in association with the Collection as defined by the contributing researcher, as well as the dates for the expected initial upload of the data, and when it is first expected to be shared, or with the research community. Above the primary table of Data Expected, any publications determined to be relevant to the data within the Collection are also displayed - members of the contributing research group can use these to define NDA Studies, connecting those papers to underlying data in NDA.

The tab is used both as a reference for those accessing shared data, providing information on what is expected and when it will be shared, and as the primary tracking mechanism for contributing projects. It is used by both contributing primary researchers, secondary researchers, and NIH Program and Grants Management staff.

Researchers who are starting their project need to update their Data Expected list to include all the Data Structures they are collecting under their grant and set their initial submission and sharing schedule according to the NDA Data Sharing Regimen.

To add existing Data Structures from the Data Dictionary, to request new Data Structure that are not in the Dictionary, or to request changes to existing Data Structures, click "+New Data Expected".

For step-by-step instructions on how to add existing Data Structures, request changes to an existing Structure, or request a new Data Structure, please visit the Completing Your Data Expected Tutorial.

If you are a contributing researcher creating this list for the first time, or making changes to the list as your project progress, please note the following:

  • Although items you add to the list and changes you make are displayed, they are not committed to the system until you Save the entire page using the "Save" button at the bottom of your screen. Please Save after every change to ensure none of your work is lost.
  • If you attempt to add a new structure, the title you provide must be unique - if another structure exists with the same name your change will fail.
  • Adding a new structure to this list is the only way to request the creation of a new Data Dictionary definition.

Frequently Asked Questions

  • What is an NDA Data Structure?
    An NDA Data Structure is comprised of multiple Data Elements to make up an electronic definition of an assessment, measure, questionnaire, etc will have a corresponding Data Structure.
  • What is the NDA Data Dictionary?
    The NDA Data Dictionary is comprised of electronic definitions known as Data Structures.

Glossary

  • Analyzed Data
    Data specific to the primary aims of the research being conducted (e.g. outcome measures, other dependent variables, observations, laboratory results, analyzed images, volumetric data, etc.) including processed images.
  • Data Item
    Items listed on the Data Expected list in the Collection which may be an individual and discrete Data Structure, Data Structure Category, or Data Structure Group.
  • Data Structure
    A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure
  • Data Structure Category
    An NDA term describing the affiliation of a Data Structure to a Category, which may be disease/disorder or diagnosis related (Depression, ADHD, Psychosis), specific to data type (MRI, eye tracking, omics), or type of data (physical exam, IQ).
  • Data Structure Group
    A Data Item listed on the Data Expected tab of a Collection that indicates a group of Data Structures (e.g., ADOS or SCID) for which data may be submitted instead of a specific Data Structure identified by version, module, edition, etc. For example, the ADOS Data Structure Category includes every ADOS Data Structure such as ADOS Module 1, ADOS Module 2, ADOS Module 1 - 2nd Edition, etc. The SCID Data Structure Group includes every SCID Data Structure such as SCID Mania, SCID V Mania, SCID PTSD, SCID-V Diagnosis, and more.
  • Evaluated Data
    A new Data Structure category, Evaluated Data is analyzed data resulting from the use of computational pipelines in the Cloud and can be uploaded directly back to a miNDAR database. Evaluated Data is expected to be listed as a Data Item in the Collection's Data Expected Tab.
  • Imaging Data
    Imaging+ is an NDA term which encompasses all imaging related data including, but not limited to, images (DTI, MRI, PET, Structural, Spectroscopy, etc.) as well as neurosignal data (EEG, fMRI, MEG, EGG, eye tracking, etc.) and Evaluated Data.
  • Initial Share Date
    Initial Submission and Initial Share dates should be populated according to the NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data will be shared with authorized users upon publication (via an NDA Study) or 1-2 years after the grant end date specified on the first Notice of Award, as defined in the applicable Data Sharing Terms and Conditions.
  • Initial Submission Date
    Initial Submission and Initial Share dates should be populated according to these NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data for all subjects is not expected on the Initial Submission Date and modifications may be made as necessary based on the project's conduct.
  • Research Subject and Pedigree
    An NDA created Data Structure used to convey basic information about the subject such as demographics, pedigree (links family GUIDs), diagnosis/phenotype, and sample location that are critical to allow for easier querying of shared data.
  • Submission Cycle
    The NDA has two Submission Cycles per year - January 15 and July 15.
  • Submission Exemption
    An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Associated Studies

Studies that have been defined using data from a Collection are important criteria to determine the value of data shared. The number of subjects column displays the counts from this Collection that are included in a Study, out of the total number of subjects in that study. The Data Use column represents whether or not the study is a primary analysis of the data or a secondary analysis. State indicates whether the study is private or shared with the research community.

Study NameDOIAbstractCollection/Study SubjectsData UsageState
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.10.15154/7wf7-3479Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.485/485Primary AnalysisShared
Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain.10.15154/82za-1n05Genomic regulatory elements active in the developing human brain are notably enriched in genetic risk for neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and bipolar disorder. However, prioritizing the specific risk genes and candidate molecular mechanisms underlying these genetic enrichments has been hindered by the lack of a single unified large-scale gene regulatory atlas of human brain development. Here, we uniformly process and systematically characterize gene, isoform, and splicing quantitative trait loci (xQTLs) in 672 fetal brain samples from unique subjects across multiple ancestral populations. We identify 15,752 genes harboring a significant xQTL and map 3,739 eQTLs to a specific cellular context. We observe a striking drop in gene expression and splicing heritability as the human brain develops. Isoform-level regulation, particularly in the second trimester, mediates the greatest proportion of heritability across multiple psychiatric GWAS, compared with eQTLs. Via colocalization and TWAS, we prioritize biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, nearly two-fold that observed in the adult brain. Finally, we build a comprehensive set of developmentally regulated gene and isoform co-expression networks capturing unique genetic enrichments across disorders. Together, this work provides a comprehensive view of genetic regulation across human brain development as well as the stage-and cell type-informed mechanistic underpinnings of neuropsychiatric disorders.158/158Primary AnalysisShared
Molecular cascades and cell type-specific signatures in ASD revealed by single-cell genomics10.15154/9amm-vr95Genomic profiling in postmortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition are not well understood. We performed deep single-nucleus RNA sequencing (snRNA-seq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism spectrum disorder (ASD), which we corroborated using single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) and spatial transcriptomics. Transcriptomic changes were primarily cell type specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain.67/67Primary AnalysisShared
Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids.10.15154/gswj-jk47Regulation of gene expression through enhancers is one of the major processes shaping the structure and function of the human brain during development. High-throughput assays have predicted thousands of enhancers involved in neurodevelopment, and confirming their activity through orthogonal functional assays is crucial. Here, we utilized Massively Parallel Reporter Assays (MPRAs) in stem cells and forebrain organoids to evaluate the activity of ~ 7000 gene-linked enhancers previously identified in human fetal tissues and brain organoids. We used a Gaussian mixture model to evaluate the contribution of background noise in the measured activity signal to confirm the activity of ~ 35% of the tested enhancers, with most showing temporal-specific activity, suggesting their evolving role in neurodevelopment. The temporal specificity was further supported by the correlation of activity with gene expression. Our findings provide a valuable gene regulatory resource to the scientific community.20/20Primary AnalysisShared
* Data not on individual level
helpcenter.collection.associated-studies-tab

NDA Help Center

Collection - Associated Studies

Clicking on the Study Title will open the study details in a new internet browser tab. The Abstract is available for viewing, providing the background explanation of the study, as provided by the Collection Owner.

Primary v. Secondary Analysis: The Data Usage column will have one of these two choices. An associated study that is listed as being used for Primary Analysis indicates at least some and potentially all of the data used was originally collected by the creator of the NDA Study. Secondary Analysis indicates the Study owner was not involved in the collection of data, and may be used as supporting data.

Private v. Shared State: Studies that remain private indicate the associated study is only available to users who are able to access the collection. A shared study is accessible to the general public.

Frequently Asked Questions

  • How do I associate a study to my collection?
    Studies are associated to the Collection automatically when the data is defined in the Study.

Glossary

  • Associated Studies Tab
    A tab in a Collection that lists the NDA Studies that have been created using data from that Collection including both Primary and Secondary Analysis NDA Studies.
Edit