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CTCF HiChIP experiments in cells treatd with control shRNA or BHLHE40 shRNA

ABSTRACT: CTCF HiChIP experiments in cells treatd with control shRNA or BHLHE40 shRNA

PROVIDER: PRJNA573664 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10163455_1.fastq.gz	Fastqsanger.gz
	SRR10163455_2.fastq.gz	Fastqsanger.gz
	SRR10163456_1.fastq.gz	Fastqsanger.gz
	SRR10163456_2.fastq.gz	Fastqsanger.gz
	SRR11902169_1.fastq.gz	Fastqsanger.gz

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CTCF HiChIP experiments in cells treatd with control shRNA or BHLHE40 shRNA

Project description:In this study, we investigated CTCF mediated chromatin interactions by HiChIP experiment in control shRNA and BHLHE40-depleted HeLa-S3 cells.

2020-08-14 | GSE137849 | GEO

Genome-wide maps of CTCF and BHLHe40 binding in HeLa-S3 cells

Project description:In this study, we investigated CTCF and BHLHE40 binding in HeLa-S3 cells transfected with control shRNA and specific shRNA.

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RNA-seq of control shRNA and BHLHE40 shRNA HeLa-S3 cells

Project description:In this study, we investigated gene expression profile in HeLa-S3 cells transfected with control shRNA and BHLHE40 shRNA.

2020-08-14 | GSE137850 | GEO

CTCF HiChIP data in A673 Ewing sarcoma cell lines (siCT & siSA2)

Project description:STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. A673 Ewing sarcoma cell line was trasfected with siCT or 2 different siRNA targetting STAG2 during 72h and CTCF HiChIP experiments were preformed for each conditions. Analyses of HiChIP data show that STAG2 knowck-down alters CTCF-anchored loop extrusion.

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RNA-seq of control shRNA and BHLHE40 shRNA HeLa-S3 cells

Project description:RNA-seq of control shRNA and BHLHE40 shRNA HeLa-S3 cells

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Expression data from mouse differentiated Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells

Project description:Microarray data on TH17 cells from Bhlhe40-GFP reporter mice We used microarrays to detail the global programme of gene expression in polarized Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells Purified naÃ¯ve CD4 T cells from spleen were polarized under TH17 condition in vitro. On day 4, cells were stimulated with PMA and ionomycin, and sorted by their Bhlhe40-GFP expression prior to microarray analysis

2016-01-04 | E-GEOD-75407 | biostudies-arrayexpress

HiChIP data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)

Project description:STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma. Using a CRISPR/Cas9 approach, we generated two STAG2 knock-out isogenic clones (A673_SA2m#1 and TC71_SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. A STAG2 rescue model (A673_SA2r) was generated by correcting the CRISPR mutation in the A673_SA2m#1 model. These STAG1/2 proficient and deficient models were profiled by CTCF HiChIP experiments. STAG2 isogenic models were also profiled by H3K27ac HiChIP experiments. Analyses of HiChIP data allowed to show that STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions.

2021-04-29 | GSE133227 | GEO

Expression data from mouse differentiated Bhlhe40-GFPneg and Bhlhe40-GFPpos TH17 cells

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Genome-wide maps of CTCF and BHLHe40 binding in HeLa-S3 cells

Project description:Genome-wide maps of CTCF and BHLHe40 binding in HeLa-S3 cells

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MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Project description:Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.

2019-04-05 | GSE119663 | GEO

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