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Series GSE81026 Query DataSets for GSE81026
Status Public on Apr 17, 2017
Title Cis Regulatory Element Scan by Tiling-deletion and Sequencing
Organisms Homo sapiens; synthetic construct
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Here we report a highly scalable strategy for unbiased discovery and functional characterization of cis regulatory elements in the genome. These results demonstrate the utility of our cis element discovery strategy and reveal the dual function of gene promoters: they not only initiate transcription of their own genes, but could also control transcription of nearby genes.
Overall design As proof of principle, we focused on the 2Mbp POU5F1 locus (hg19 chr6:30120000-32150000) in hESCs with the goal to identify cis-regulatory elements involved in the transcriptional control of POU5F1. We first designed 11,570 sgRNA pairs that would introduce ~2kb-deletions in a highly nested manner with ~100bp step sizes. As negative controls, we included 424 ineffective oligos lacking the PAM sequence necessary for effective dsDNA breaks. Additionally, we also included 6 sgRNA pairs that target the eGFP coding sequence as positive controls. The dual CRISPR expressing cassettes were cloned into lentiCRISPRv2 vector, and the resulting lentiviral libraries were verified to be of high quality and capable of generating genomic deletions.

ATAC-seq is a widely used method to mapping the open chromatin landscape of the cells. In this study, we perfomed ATAC-seq to compare the open chromain patters in wild-type and two mutant clones with PRRC2A and MSH5 core promoter region deletions. The core promoters of PRRC2A and MSH5 have been identified as distal enhancer of POU5F1 and we want to test if and how the deletion of distal enhancer affect the open chromaitn patterns.
Contributor(s) Diao Y, Fang R, Li B, Meng Z, Marina RJ, Jung I, Guan K, Ren B
Citation(s) 28417999
Submission date May 02, 2016
Last update date May 15, 2019
Contact name Bing Ren
Organization name University of California, San Diego School of Medicine
Street address 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21616 Illumina HiSeq 4000 (synthetic construct)
Samples (23)
GSM2140798 Cis_1
GSM2140799 Cis_2
GSM2140800 Cis_3
BioProject PRJNA320305
SRA SRP074253

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

Supplementary file Size Download File type/resource
GSE81026_4cseq_pipe_manual.pdf.gz 188.4 Kb (ftp)(http) PDF
GSE81026_CREST_peaks.bed.gz 391 b (ftp)(http) BED
GSE81026_RAW.tar 2.3 Gb (http)(custom) TAR (of BW, TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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