brainSCOPE: Brain Single-Cell Omics for PsychEncode Resource
This website hosts all raw data and output files associated with the brainSCOPE Resource, which incorporates single cell-resolution, multi-omic data for 388 adult DLPFC samples. Additional details for these files are described in the manuscript supplement.

Key Resources

We offer a select list of brainSCOPE Resources, derived from our primary analyses, to ensure quick, easy, and fully open-source access for end users Click here to access these Key Resource files. These include sample metadata, expression quantification, scCRE regions, DE genes, gene variance, scQTL callsets, GRNs, cell-to-cell networks, and predictive model results.

Raw Data

Raw data files for PsychEncode single-cell samples, including FASTQs for snRNA-Seq, snATAC-Seq, snMultiome, and genotype data, are hosted with protected access at the Synapse data repository and other repositories. Links and descriptions for each individual dataset are available here.

Output Files

All output files from brainSCOPE-related analyses, including the resource files and expanded analyses, as well as computer code used in the analyses are available for download here. These datasets are fully open-source.

Interactive Visualization

Select brainSCOPE datasets, such as snRNA-Seq, scQTLs, and gene regulatory networks, can be visualized within the PsychSCREEN Single-Cell Browser. Click here to view examples for each visualization tool within PsychSCREEN.

Source Code

Source code for snRNA-Seq data processing, scQTL detection pipelines, and deep learning model implementation used in the integrative analysis is available at the PsychENCODE GitHub repository.