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Series GSE132757 Query DataSets for GSE132757
Status Public on May 05, 2020
Title CRISPR-Mediated Multiplexed Epigenomic Perturbation of Putatively Functional ASoC Sites in Human Neural Progenitor Cell Model at Single-cell Resolution
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Functional interpretation of noncoding disease variants, which likely regulate gene expression, has been challenging. Chromatin accessibility (openness) strongly influences gene expression in neurodevelopment; however, to what extent genetic variants can alter chromatin openness in the context of brain disorders/traits is largely unknown. Using human induced pluripotent stem cell (iPSC)-derived neurons as a neurodevelopmental model, we identified abundant open-chromatin regions absent in brains and thousands of genetic variants exhibiting allele-specific open-chromatin (ASoC). ASoC variants are overrepresented in brain enhancers, transcription-factor-binding sites, and quantitative-trait-loci affecting histone modifications or DNA methylation. ASoC variants are also highly enriched for those associated with brain disorders/traits. Following-up schizophrenia-associated ASoC variants by multiplex epigenomic perturbation, computational fine-mapping, and CRISPR-editing further confirmed their regulatory activities and cis-targeted genes. Our study provides the first snapshot of neuronal ASoC landscape and a framework for prioritizing functional disease variants.
Overall design NPC samples were derived from individual cell line #05, #07, and #08. Collected NPC samples were processed with 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions. Sequencing of the prepared library was performed on an Illumina sequencer generating approximately 450M reads in total.
Contributor(s) Duan J, Zhang S
Citation(s) 32732423, 34308291
Submission date Jun 14, 2019
Last update date Jul 28, 2021
Contact name Jubao Duan
Phone (224) 364-7564
Organization name NorthShore University HealthSystem
Department Center for Psychiatric Genetics
Lab Unit of Functional Genomics in Psychiatry
Street address 1001 University Place
City Evanston
State/province IL
ZIP/Postal code 60201
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (2)
GSM3891464 CRISPRi-scRNA-Seq (NPC_05_07)
GSM3891465 CRISPRi-scRNA-Seq (NPC_08)
BioProject PRJNA548928
SRA SRP201467

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE132757_filtered_gene_bc_matrices_h5.h5 29.1 Mb (ftp)(http) H5
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Raw data are available in SRA
Processed data are available on Series record

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