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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

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)

Submission date

Dec 11, 2018

Last update date

Jul 05, 2022

Contact name

ya wei song

E-mail(s)

song_yawei@gibh.ac.cn

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)

More...

GSM3508537	D10_oecontrol_rep1 [RNA-seq]
GSM3508538	D10_oecontrol_rep2 [RNA-seq]
GSM3508539	D10_oeCTCF_rep1 [RNA-seq]

GSM3508540	D10_oeCTCF_rep2 [RNA-seq]
GSM3508541	D10_oeCTCF&shSmarca5_rep1 [RNA-seq]
GSM3508542	D10_oeCTCF&shSmarca5_rep2 [RNA-seq]
GSM3508543	D10_shcontrol_rep1 [RNA-seq]
GSM3508544	D10_shcontrol_rep2 [RNA-seq]
GSM3508545	D10_shCTCF_rep1 [RNA-seq]
GSM3508546	D10_shCTCF_rep2 [RNA-seq]
GSM3508547	MEFs [RNA-seq]
GSM3508548	iPSCs [RNA-seq]
GSM4976366	D0_shLuci_rep1 [RNA-seq]
GSM4976367	D0_shLuci_rep2 [RNA-seq]
GSM4976368	D0_shCTCF_rep1 [RNA-seq]
GSM4976369	D0_shCTCF_rep2 [RNA-seq]
GSM4976370	D3_shLuci_Thy1+_rep1 [RNA-seq]
GSM4976371	D3_shLuci_Thy1+_rep2 [RNA-seq]
GSM4976372	D3_shCTCF_Thy1+_rep1 [RNA-seq]
GSM4976373	D3_shCTCF_Thy1+_rep2 [RNA-seq]
GSM4976374	D3_shLuci_SSEA1+_rep1 [RNA-seq]
GSM4976375	D3_shLuci_SSEA1+_rep2 [RNA-seq]
GSM4976376	D3_shCTCF_SSEA1+_rep1 [RNA-seq]
GSM4976377	D3_shCTCF_SSEA1+_rep2 [RNA-seq]
GSM4976378	D3_shLuci_SSEA1-Thy1-_rep1 [RNA-seq]
GSM4976379	D3_shLuci_SSEA1-Thy1-_rep2 [RNA-seq]
GSM4976380	D3_shCTCF_SSEA1-Thy1-_rep1 [RNA-seq]
GSM4976381	D3_shCTCF_SSEA1-Thy1-_rep2 [RNA-seq]
GSM4976382	D6_shLuci_Thy1+_rep1 [RNA-seq]
GSM4976383	D6_shLuci_Thy1+_rep2 [RNA-seq]
GSM4976384	D6_shCTCF_Thy1+_rep1 [RNA-seq]
GSM4976385	D6_shCTCF_Thy1+_rep2 [RNA-seq]
GSM4976386	D6_shLuci_SSEA1+_rep1 [RNA-seq]
GSM4976387	D6_shLuci_SSEA1+_rep2 [RNA-seq]
GSM4976388	D6_shCTCF_SSEA1+_rep1 [RNA-seq]
GSM4976389	D6_shCTCF_SSEA1+_rep2 [RNA-seq]
GSM4976390	D6_shLuci_SSEA1-Thy1-_rep1 [RNA-seq]
GSM4976391	D6_shLuci_SSEA1-Thy1-_rep2 [RNA-seq]
GSM4976392	D6_shCTCF_SSEA1-Thy1-_rep1 [RNA-seq]
GSM4976393	D6_shCTCF_SSEA1-Thy1-_rep2 [RNA-seq]
GSM4976394	D9_shLuci_Thy1+_rep1 [RNA-seq]
GSM4976395	D9_shLuci_Thy1+_rep2 [RNA-seq]
GSM4976396	D9_shCTCF_Thy1+_rep1 [RNA-seq]
GSM4976397	D9_shCTCF_Thy1+_rep2 [RNA-seq]
GSM4976398	D9_shLuci_SSEA1+_rep1 [RNA-seq]
GSM4976399	D9_shLuci_SSEA1+_rep2 [RNA-seq]
GSM4976400	D9_shCTCF_SSEA1+_rep1 [RNA-seq]
GSM4976401	D9_shCTCF_SSEA1+_rep2 [RNA-seq]
GSM4976402	D9_shLuci_SSEA1-Thy1-_rep1 [RNA-seq]
GSM4976403	D9_shLuci_SSEA1-Thy1-_rep2 [RNA-seq]
GSM4976404	D9_shCTCF_SSEA1-Thy1-_rep1 [RNA-seq]
GSM4976405	D9_shCTCF_SSEA1-Thy1-_rep2 [RNA-seq]
GSM4976406	D12_shLuci_GFP+_rep1 [RNA-seq]
GSM4976407	D12_shLuci_GFP+_rep2 [RNA-seq]
GSM4976408	D12_shCTCF_GFP+_rep1 [RNA-seq]
GSM4976409	D12_shCTCF_GFP+_rep2 [RNA-seq]

This SubSeries is part of SuperSeries:

CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

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
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record

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