EXPERIMENT_TITLE: GSM3106839: PCHiC_human primary fetal astrocytes_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were harvested, fixed in 1% formaldehyde, then stored at -80C.  Nuclei extraction was performed prior to further processing. In situ Hi-C was performed using the standard protocol, then the resulting libraries were used to prepare promoter capture Hi-C libraries using a custom biotinylated RNA probe set.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: 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)
SAMPLE_TITLE: PCHiC_human primary fetal astrocytes_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human primary fetal astrocytes"}, {"TAG": "cell type", "VALUE": "human primary fetal astrocytes"}]
Pool_Member_@attributes_sample_title: PCHiC_human primary fetal astrocytes_rep2
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