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Series GSE120648 Query DataSets for GSE120648
Status Public on Dec 27, 2018
Title The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Human primordial germ cells (hPGCs) are the first embryonic progenitors in the germ cell lineage, yet the molecular mechanisms required for hPGC formation are not well characterized. To identify regulatory regions in hPGC development, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to systematically characterize regions of open chromatin in hPGCs and hPGC-like cells (hPGCLCs) differentiated from human embryonic stem cells (hESCs). We discovered regions of open chromatin unique to hPGCs and hPGCLCs that significantly overlap with TFAP2C-bound enhancers identified in the naive ground state of pluripotency. Using CRISPR/Cas9, we show that deleting the TFAP2C-bound naive enhancer at the OCT4 locus (also called POU5F1) results in impaired OCT4 expression and a negative effect on hPGCLC identity.
 
Overall design 26 ATAC-seq libraries: 9 ATAC-seq libraries from primed hESCs, 4 ATAC-seq libraries from iMeLC induced from primed hESCs, 3 ATAC-seq libraries from hPGCLCs induced from primed hESCs, 6 ATAC-seq libraries from sorted hPGCs, 4 ATAC-seq libraries from liver, lung, skin and heart cells from human embryo.
 
Contributor(s) Chen D, Liu W
Citation(s) 30590035
Submission date Sep 28, 2018
Last update date Mar 27, 2019
Contact name Wanlu Liu
Organization name Zhejiang University
Department Zhejiang University - University of Edinburgh Institute
Lab Wanlu Liu
Street address 718 East Haizhou Rd.,
City Haining
State/province Zhejiang
ZIP/Postal code 314400
Country China
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (26)
GSM3406929 ATACseqUCLA1hESCrep1
GSM3406930 ATACseqUCLA1hESCrep2
GSM3406931 ATACseqUCLA2hESCrep1
Relations
BioProject PRJNA493830
SRA SRP162878

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

Supplementary file Size Download File type/resource
GSE120648_RAW.tar 2.3 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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