Brain Single-Cell Omics for PsychEncode (brainSCOPE)
Raw Data

This webpage contains data matrices linking to all raw sequencing data files in the brainSCOPE Resource, including snRNA-Seq, snATAC-Seq, snMultiome, and genotype data (SNP microarray, WGS, or exome sequencing).

Raw sequencing datasets (fastq files) for samples from PsychEncode Consortium cohorts are hosted on Synapse under protected access. VCF files for imputed genotypes of all PsychEncode samples are also hosted on Synapse. The main Synapse repository containing the FASTQ files and processed data for this study can be accessed here. Please note that users must create a Synapse account and log in to view individual datasets.

Links are also provided below for raw datasets from external cohorts; i.e. ROSMAP samples that are hosted in the AMP-AD Knowlegde Portal.

Please see the supplementary of the associated manuscript for more details on how these files were generated.

Constructing a single-cell genomic resource for 388 individuals

26K	.txt	PEC2_sample_metadata.txt	Clinical and demographic meta-data for each sample in the brainSCOPE resource.
34K	.XLSX	raw_sequencing_data_links.xlsx	This file contains links and accession numbers for snRNA-seq, snATAC-Seq, and genotype data that are publically available on Synapse or other repositories. Non-PEC samples that are not publically available are labeled "Non-PEC".
41G	.h5ad	Gene expression quantification datasets (Synapse)	Link to .H5AD files with processed scRNA-Seq datasets for all PsychEncode Consortium samples. .H5AD files are stored in directores by cohort, which also contain metadata files as well as count matrices for each sample.
97M	.VCF	brainSCOPE_PEC_sample_genotypes_with_rna.vcf	This link provides access to the Synapse directory that hosts uniformly-processed imputed genotypes for 226 PsychEncode-derived samples.
94M	.VCF	brainSCOPE_PEC_sample_genotypes_no_rna.vcf	This link provides access to the Synapse directory that hosts imputed genotypes for 218 PsychEncode-derived samples, excluding snRNA-Seq derived genotypes.
		Link to AMP-AD Knowledge Portal	This link provides access to the AMP-AD Knowledge Portal page that hosts uniformly-processed snRNA-Seq data and imputed genotypes for 48 ROSMAP samples used in PsychENCODE analysis.

Raw data file list

snRNA-seq

Cohort	Link to snRNA-seq files
CMC	CMC snRNA-seq	This link leads to the Synapse page with all CMC snRNA-seq fastq files.
DevBrain-snRNAseq	DevBrain-snRNAseq snRNA-seq	This link leads to the Synapse page with all DevBrain-snRNAseq fastq files.
IsoHuB	IsoHuB snRNA-seq	This link leads to the Synapse page with all IsoHuB snRNA-seq fastq files.
Velmeshev	Velmeshev snRNA-seq	This link leads to the NCBI GEO page with all Velmeshev snRNA-seq fastq files.
LIBD	LIBD snRNA-seq	This link leads to the Synapse page with all LIBD snRNA-seq fastq files.
Ma-Sestan	Ma-Sestan snRNA-seq	This link leads to the NeMO Archive page with all Ma-Sestan snRNA-seq fastq files.
PTSDBrainomics	PTSDBrainomics snRNA-seq	This link leads to the Synapse page with all PTSDBrainomics snRNA-seq fastq files.
ROSMAP	ROSMAP snRNA-seq	This link leads to the Synapse page with all ROSMAP snRNA-seq fastq files.
SZBDMulti-Seq	SZBDMulti-Seq snRNA-seq	This link leads to the Synapse page with all SZBDMulti-Seq snRNA-seq fastq files.
UCLA-ASD	UCLA-ASD snRNA-seq	This link leads to the Synapse page with all UCLA-ASD snRNA-seq fastq files.
MultiomeBrain	MultiomeBrain snRNA-seq	This link leads to the Synapse page with all MultiomeBrain snRNA-seq fastq files.
Girgenti-Multiome	Girgenti-snMultiome snRNA-seq	This link leads to the NCBI GEO page with all Girgenti snMultiome fastq files.

Genotype

Cohort	Link to genotype files
CMC	CMC Genotype	This link leads to the Synapse page with all CMC microarray genotype files.
DevBrain-snRNAseq	DevBrain-snRNAseq Genotype	This link leads to the Synapse page with 7/16 DevBrain-snRNAseq RNA-based genotype files.
DevBrain-snRNAseq	DevBrain-snRNAseq Genotype	This link leads to the Synapse page with 1/16 DevBrain-snRNAseq WGS-based genotype files.
IsoHuB	IsoHuB Genotype	This link leads to the Synapse page with 1/4 IsoHuB RNA-based genotype files.
IsoHuB	IsoHuB Genotype	This link leads to the Synapse page with 3/5 IsoHuB microarray genotype files.
Velmeshev	Velmeshev Genotype	This link leads to the NCBI GEO page with all Velmeshev genotype files (exome and RNA-based).
LIBD	LIBD Genotype	This link leads to the Synapse page with all LIBD microarray genotype files.
Ma-Sestan	Ma-Sestan Genotype	This link leads to the NeMO Archive page with 2/4 Ma-Sestan RNA-based genotype files.
	Ma-Sestan Genotype	This link leads to the Synapse page with 1/4 Ma-Sestan RNA-based genotype files.
	Ma-Sestan Genotype	This link leads to the Synapse page with 1/4 Ma_et_al WGS-based genotype files.
PTSDBrainomics	PTSDBrainomics Genotype	This link leads to the Synapse page with all PTSDBrainomics microarray genotype files.
ROSMAP	ROSMAP Genotype	This link leads to the Synapse page with 3/46 ROSMAP RNA-based genotype files.
	ROSMAP Genotype	This link leads to the Synapse page with 37/46 ROSMAP WGS-based genotype files.
	ROSMAP Genotype	This link leads to the Synapse page with 5/46 ROSMAP microarray genotype files.
	ROSMAP Genotype	This link leads to the Synapse page with 1/46 ROSMAP microarray genotype files.
SZBDMulti-Seq	SZBDMulti-Seq Genotype	This link leads to the Synapse page with all SZBDMulti-Seq microarray genotype files.
UCLA-ASD	UCLA-ASD Genotype	This link leads to the Synapse page with 15/53 UCLA-ASD microarray genotype files.
UCLA-ASD	UCLA-ASD Genotype	This link leads to the Synapse page with 1/53 UCLA-ASD RNA-based genotype files.