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Series GSE113481 Query DataSets for GSE113481
Status Public on Jun 15, 2019
Title Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [PCHiC]
Organism Homo sapiens
Experiment type Other
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 pcHi-C on iPSC-induced excitatory neurons (3 replicates), iPSC-derived hippocampal dentate gyrus (DG)-like neurons (2 replicates), iPSC-induced lower motor neurons (3 replicates), and human primary fetal astrocytes (4 replicates)
Contributor(s) Song M, Shen Y
Citation(s) 31367015
Submission date Apr 20, 2018
Last update date Sep 04, 2019
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 (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM3106832 PCHiC_iPSC-induced excitatory neurons_rep1
GSM3106833 PCHiC_iPSC-induced excitatory neurons_rep2
GSM3106834 PCHiC_iPSC-induced excitatory neurons_rep3
This SubSeries is part of SuperSeries:
GSE113483 Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes
BioProject PRJNA451216
SRA SRP141473

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Supplementary file Size Download File type/resource
GSE113481_RAW.tar 6.7 Gb (http)(custom) TAR (of TXT)
GSE113481_wtc_PASS_hg19.phased_v2.vcf.gz 177.3 Mb (ftp)(http) VCF
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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