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Series GSE123641 Query DataSets for GSE123641
Status Public on Apr 05, 2022
Title CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary CCCTC binding factor (CTCF) has been implicated in mediating chromatin insulation and long-distance interactions between enhancer and promoter. In this study, to study the roles of CTCF in somatic cell reprogramming, we performed RNA-seq, Hi-C, ChIP-seq and ATAC-seq at the specific stage of reprogramming. Through bioinformatics analysis, our data indicated that CTCF promotes enhancer-promoter interactions and chromatin accessibility to regulate the expression of key pluripotency genes; meanwhile, it serves as an insulator to suppress the expression of key somatic genes. Smarca5 loss inhibits CTCF-promoted reprogramming by reversing CTCF insulator activity on MEF-specific genes and leading to incorrect nucleosome positioning adjacent to CTCF binding sites. These findings reveal the dual functions of CTCF as both a structural regulator and insulator in conjunction with a key chromatin remodeler to drive cellular reprogramming towards pluripotency.
Overall design Gene expression profiling of reprogramming cells with OSKM plus control, OSKM plus Ctcf overexpression, OSKM with Ctcf overexpression plus Smarca5 knockdown on day 10. Gene expression profiling of reprogramming cells with OSKM plus control or Ctcf shRNA on day 10. Gene expression profiling of mouse embryonic fibroblast (MEF) cells, iPSCs, sorted reprogramming intermediate cells in the TetOn lentivirus OSKM reprogramming system with both control shRNA and Ctcf knockdown.
Contributor(s) Hutchins AP, Liang Z, Hu G, Song Y
Citation(s) 35385732
Submission date Dec 11, 2018
Last update date Jul 05, 2022
Contact name ya wei song
Phone 13288824450
Organization name Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences
Department South China Institute for Stem Cell Biology and Regenerative Medicine
Street address 190 Kai Yuan Avenue, Science Park
City Guangzhou
State/province Guangdong
ZIP/Postal code 510530
Country China
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (56)
GSM3508537 D10_oecontrol_rep1 [RNA-seq]
GSM3508538 D10_oecontrol_rep2 [RNA-seq]
GSM3508539 D10_oeCTCF_rep1 [RNA-seq]
This SubSeries is part of SuperSeries:
GSE123670 CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming
BioProject PRJNA509452
SRA SRP173291

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
GSE123641_MEF_iPS_RNAseq.tsv.gz 308.9 Kb (ftp)(http) TSV
GSE123641_rnaseq_oectcf_d10.tsv.gz 2.0 Mb (ftp)(http) TSV
GSE123641_rnaseq_oectcf_shsmarca5_d10_ntc.tsv.gz 286.6 Kb (ftp)(http) TSV
GSE123641_rnaseq_shctcf_d10.tsv.gz 2.1 Mb (ftp)(http) TSV
GSE123641_rnaseq_stage_expression_rnaseq_ntc.tsv.gz 1.3 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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