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Series GSE126211 Query DataSets for GSE126211
Status Public on Jun 15, 2019
Title Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [CUT&RUN]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Mutations in gene regulatory elements have been associated with a wide range of complex neuropsychiatric disorders. However, due to their cell-type specificity and difficulties in characterizing their regulatory targets, the ability to identify causal genetic variants has remained limited. To address these constraints, we perform an integrative analysis of chromatin interactions, open chromatin regions and transcriptomes using promoter capture Hi-C, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing, respectively, in four functionally distinct neural cell types: induced pluripotent stem cell (iPSC)-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus-like neurons and primary astrocytes. We identify hundreds of thousands of long-range cis-interactions between promoters and distal promoter-interacting regions, enabling us to link regulatory elements to their target genes and reveal putative processes that are dysregulated in disease. Finally, we validate several promoter-interacting regions by using clustered regularly interspaced short palindromic repeats (CRISPR) techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP and DRD2 are transcriptionally regulated by physically linked enhancers.
Overall design H3K27ac and CTCF CUT&RUN on iPSC-induced excitatory neurons (1 replicates) and iPSC-induced lower motor neurons (2 replicates)
Contributor(s) Song M, Shen Y
Citation(s) 31367015
Submission date Feb 07, 2019
Last update date Apr 08, 2021
Contact name Yin Shen
Phone 4155023403
Organization name UCSF
Department Department of Neurology
Lab Shen Lab
Street address 513 Parnassus Ave
State/province CALIFORNIA
ZIP/Postal code 94143-0410
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (6)
GSM3593769 CUT&RUN-H3K27ac_iPSC-induced lower motor neurons_rep1
GSM3593770 CUT&RUN-CTCF_iPSC-induced lower motor neurons_rep1
GSM3593771 CUT&RUN-H3K27ac_iPSC-induced lower motor neurons_rep2
This SubSeries is part of SuperSeries:
GSE113483 Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
BioProject PRJNA521322
SRA SRP184484

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

Supplementary file Size Download File type/resource 485.0 Mb (ftp)(http) BW
GSE126211_IJ195.hg19.nuc.nodups.0.05_peaks.narrowPeak.gz 1.3 Mb (ftp)(http) NARROWPEAK 191.8 Mb (ftp)(http) BW
GSE126211_IJ196.hg19.nuc.nodups.0.05_peaks.narrowPeak.gz 406.6 Kb (ftp)(http) NARROWPEAK
GSE126211_MN.CTCF.merged.0.05_peaks.narrowPeak.gz 1.0 Mb (ftp)(http) NARROWPEAK 407.3 Mb (ftp)(http) BW
GSE126211_MN.H3K27ac.merged.0.05_peaks.narrowPeak.gz 1.9 Mb (ftp)(http) NARROWPEAK 516.7 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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