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Series GSE246791 Query DataSets for GSE246791
Status Public on Nov 02, 2023
Title Single-cell analysis of chromatin accessibility in the adult mouse brain
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated through examination of the chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1482 distinct brain cell populations, adding over 446,000 new cCREs to the most recent such annotation in the mouse genome. Raw fastq files are demultiplexed. Out of 234 samples, fastq files for 6 samples are available in NCBI under the accession number GSE126724 (CEMBA180308_3B, CEMBA180312_3B, CEMBA180226_1A, CEMBA180227_1A, CEMBA180305_2B, CEMBA180306_2B). Processed data are SnapATAC2 (<= 2.4.0) h5ad files per sample, with raw fragments and 500-bp bmat. NOTE: due to the break changes in SnapATAC2 >= 2.5.0, the data can not be handled rightly in SnapATAC2 >= 2.5.0.
Overall design We generated single-nucleus assys for transposase-accessible chromatin using sequencing (snATAC-seq) libraries from 117 anatomic dissections of mouse brain and two replicates for each dissection.
Web link
Contributor(s) Zu S, Li YE, Lee S, Preissl S, Ren B
Citation(s) 38092917
NIH grant(s)
Grant ID Grant title Affiliation Name
U19 MH114831 Center for Epigenomics of the Mouse Brain Atlas (CEMBA) THE SALK INSTITUTE FOR BIOLOGICAL STUDIES Joseph R Ecker
U19 MH114830 A comprehensive whole-brain atlas of cell types in the mouse ALLEN INSTITUTE Hongkui Zeng
BioProject PRJNA1033582
Submission date Nov 01, 2023
Last update date Dec 15, 2023
Contact name Songpeng Zu
Organization name University of California San Diego
Department Department of Cellular and Molecular Medicine
Lab Prof. Bing Ren Lab
Street address 9500 Gilman Dr
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (228)
GSM7876880 9L,rep1
GSM7876881 6F,rep1
GSM7876882 9L,rep2

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE246791_RAW.tar 149.8 Gb (http)(custom) TAR (of H5AD)
GSE246791_README.txt 874 b (ftp)(http) TXT 8.5 Kb (ftp)(http) CSV
GSE246791_wmb_SnapATAC2_anndata.tar.gz 117.7 Gb (ftp)(http) TAR
GSE246791_wmb_bigwigs.tar.gz 233.1 Gb (ftp)(http) TAR
GSE246791_wmb_enhancer.tar.gz 16.8 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

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