Resources
Portals to PsychENCODE Data
Embedded Files
A comprehensive catalog of genetic and epigenetic knowledge about the human brain. It was designed and built by Dr. Zhiping Weng's lab at UMass Chan Medical School as a product of the PsychENCODE Consortium.
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.
This study provides xQTL maps of the developing human brain and uncovers candidate neuropsychiatric risk mechanisms.
the ASD Single-Cell Gene Expression Portal (ASD scGENE Portal)! This browser permits the interactive querying of case-control single-cell expression presented in Wamsley et al. 2023. This data set represents the filtered data set with nearly 600k nuclei across 33 ASD and 31 control subjects.
Spatially resolved and single nucleus transcriptomics data from the dorsolateral prefrontal cortex (DLPFC) from postmortem human brain samples.
An integration of data across the phase one capstone projects to build a model taking QTLs as inputs and providing both phenotype predictions as well as functional modules involved.
IsoPropeller:
IsoPropeller:
The isoPropeller framework provides an end-to-end solution including read processing, quality control, and reference-free transcript model reconstruction across biological replicates, followed by quantification, high-stringency filtering, and functional annotation.
IsoPropeller: The core standalone command-line utilities used by the collapse and annotate analysis workflows.
IsoPropeller-collapse: Snakemake workflow to process long-read fastq/bam files, RNA isoform discovery, and QC.
IsoPropeller-annotate Snakemake workflow for functional annotation of isoforms and coding sequences.
Open-source R software package implementing the isoTWAS framework; includes vignettes, simulated data examples, and integration tutorials with major GWAS resources.
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)
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