Embedded Files
The NIMH Data Repository (NDA) is the primary home for psychENCODE data. Legacy data transfer from Synapse to NDA is now complete. A search tool is provided here to help locate data previously hosted on Synapse. Please visit the PsychENCODE landing page on NDA for a list of currently available data, including new data as it is produced by the Consortium.
PEC NDA Collections
PEC NDA Collections
The table below outlines the PsychENCODE NDA Collections. Each Collection ID links directly to that Collection’s page, where you can:
View basic study information under the General tab.
See what data is currently available under the Shared tab.
Note: If no data appear under the Shared tab, the investigators are still submitting data.
PEC data are stored across two NDA permission groups:
PsychENCODE (PEC) – all collections except one.
NDA-DS (Autism and Related Neurodevelopmental Conditions)-PUB – applies only to C5230: Mapping human brain cell type-specific isoform usage in ASD.
You must submit a separate Data Access Request (DAR) for each permission group you need. Click here for instructions to request access.
Collection Title / PI
Collection
Permission Group
Description
PsychENCODE Collection / Zhiping Weng and Mark Gerstein
PsychENCODE (PEC)
Hi-C, Bisulfite Sequencing, ChIPseq, SNP array, RNAseq, ATACSeq, proteomics and NOMEseq data from multiple brain regions and multiple neuropsychiatric disorders.
CommonMind Consortium / Panos Roussos
PsychENCODE (PEC)
RNAseq, single cell RNAseq, ATACseq, genotyping, and FANS-sorted RNAseq from multiple brain regions in Schizophrenia, Bipolar Disorder, and other neuropsychiatric disorders.
Laminar dissection of cortical human brain gene expression in neuropsychiatric disorders / Keri Martinowich
PsychENCODE (PEC)
single nuclei RNA, genotyping, and Visium spatial data of dorsolateral prefrontal cortex from individuals with Schizophrenia, Bipolar Disorder, Major Depressive Disorder, and Autism Spectrum Disorder, and matched neurotypical controls.
Integrated, cell type specific functional genomics analyses of regulatory sequence elements and their dynamic interaction networks in neuropsychiatric brain tissues / Alexander Urban
PsychENCODE (PEC)
Single cell ATACseq, Hi-ChIP, single cell RNAseq, long-read RNAseq, and proteomics in Autism Spectrum Disorder, Schizophrenia, Bipolar Affective Disorder, matched neurotypical controls, and individuals with known CNVs. Key disease relevant anatomical regions of adult and fetal brains.
Integrative Genomic Analysis of Human Brain Development and Autism / Daniel Geschwind
PsychENCODE (PEC)
RNAseq, ChIPseq, and HiC data from Autism Spectrum Disorder and neurotypical control brains. Frontal cortex, temporal cortex, and striatum across five major epochs representing disease-relevant stages in human brain development.
Next steps for PTSD genomics: from loci to function / Nikolaos Daskalakis
PsychENCODE (PEC)
Single nuclei RNAseq and Multiome-seq from Post-traumatic Stress Disorder amygdala, hippocampus and prefrontal cortex. SNP-specific CRISPR-editing of induced pluripotent stem cell (iPSC) derived neural cultures exposed to glucocorticoids.
Sex-specific trajectories in epigenomic regulation of brain patterning / Flora Vaccarino
PsychENCODE (PEC)
Single cell RNAseq, WGS, bulk RNAseq, and single nuclei multiome RNA and ATACseq in Autism Spectrum Disorder and Schizophrenia brain organoids and postmortem fetal brains.
The 3D genome in transcriptional regulation across the postnatal life span, with implications for schizophrenia and bipolar disorder / Panos Roussos
PsychENCODE (PEC)
RNAseq, ATACseq, CAGE-seq, and ChIP-seq (CTCF, H3K27ac and H3K4me3) from five human cortical and subcortical regions, including isolated glutamatergic and GABAergic neuronal, as well as oligodendrocyte and astrocyte nuclei. Cell-type specific annotations for gene expression and enhancer RNA.
High-resolution mapping of cell type-specific DNA (hydroxy)methylation in the human brain during postnatal development and in psychiatric disease / Stella Dracheva, Eran Mukamel, Chunyu Liu
PsychENCODE (PEC)
Whole genome bisulfite sequencing, oxidative bisulfite sequencing, histone modification chromatin immunoprecipitation (ChIP) sequencing, and RNA sequencing in glutamatergic and GABAergic neuron populations sorted using FANS from neurotypical human postmortem DLPFC .
Mapping human brain cell type-specific isoform usage in ASD / Dalila Pinto
NDA-DS(Autism and Related Neurodevelopmental Conditions)-PUB
Single cell RNAseq, SNP-Array, and SMARTseq data from prefrontal cortex, hippocampus, and striatum from individuals with Autism Spectrum Disorder and neurotypical controls.
Mapping the role of long noncoding RNAs in gene regulatory networks in schizophrenia / Dalila Pinto
PsychENCODE (PEC)
Long-read RNAseq from prefrontal cortex of adult individuals with Schizophrenia and neurotypical controls, cerebellum of neurotypical adult controls, and Clontech brain RNA pools.
How to Request Access to PsychENCODE Data
How to Request Access to PsychENCODE Data
To request access to PsychENCODE data, follow these steps:
Check Eligibility
Before requesting access, confirm that you and your institution meet the eligibility criteria..Submit Your Data Access Requests (DARs)
Submit a Data Access Request (DAR) for each permission group via your Data Permissions Dashboard:If you need all PsychENCODE data, you must submit two separate DARs for the following permission groups:
PsychENCODE (PEC)
Note: Use of PsychENCODE (PEC) permission group 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).
NDA-DS (Autism and Related Neurodevelopmental Conditions)-PUB
If you do not need access to Collection C5230 (Mapping human brain cell type-specific isoform usage in ASD), you only need to submit a DAR for the PsychENCODE (PEC) permission group.
Use These Resources for Guidance on Submitting Your DAR:
Review and Approval
After you submit your DAR, NDA conducts an initial review before forwarding it to your Signing Official (SO) for signature and the NIH Data Access Committee (DAC) for final approval. The DAC typically completes its review within 10 business days.Approval and Data Download
Once approved, you’ll receive one year of access to the data. You can immediately begin querying and downloading data using the NDA Query Tool and NDA Download Tools.
The PsychENCODE Consortium has also generated sequencing datasets for brain samples of animal model organisms (mouse and non-human primates). These datasets are available for download from the NCBI GEO repository, at the following accessions:
-GSE225482 {https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225482} and GSE206994 {https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206994} for data from the NHP-Macaque and NHP-Chimpanzee projects (PI: Nenad Sestan).
-GSE67753 {https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67753} for data from the MouseHAL project (PI: Gregory Crawford/Patrick Sullivan}
-GSE334303 {https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE334303} for mouse CROP-Seq data (PI: Hyejung Won)
Finally, the consortium has generated de-identified, summary-level processed datasets from the collection samples, such as gene expression matrices, quantitative trait loci (QTLs), cis-candidate regulatory elements (cCREs), and gene regulatory networks (GRNs). These datasets are available to the public on the consortium’s webpage at {https://www.psychencode.org/resources}. Of note, cross-study integrative analysis of all PsychENCODE data are available at {http://resource.psychencode.org} (Phase I) and {http://brainscope.psychencode.org} (Phase II). Many of these data can be visualized using the PsychSCREEN browser at {https://psychscreen.wenglab.org/psychscreen}.
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