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Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma

ABSTRACT: Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma

PROVIDER: PRJNA549160 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9309030_1.fastq.gz	Fastqsanger.gz
	SRR9309030_2.fastq.gz	Fastqsanger.gz
	SRR9309031.fastq.gz	Fastqsanger.gz
	SRR9309032.fastq.gz	Fastqsanger.gz
	SRR9309025_1.fastq.gz	Fastqsanger.gz

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Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma

Project description:Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma

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Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma [ChIP-Seq]

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Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma [4C-Seq]

Project description:Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma [4C-Seq]

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Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma

Project description:We profiled fresh-frozen esophageal tumor and normal samples and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNASeq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. Here, we aim to compare of Eso26 cells knock down HNF4A with siRNA and control transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We also report the application of circular chromatin conformation capture (4C) sequencing technology for studying master transcription factor (HNF4A) in human esophageal adenocarcinoma cancer cell lines (Eso26). Overall design: Esophageal Cancer and normal cell lines and fresh-frozen tissues were harvested, and ChIPseq was performed using H3K27Ac and transcription factor antibodies. Eso26 cells knock down HNF4A with siRNA and control were generated by deep sequencing, in triplicate, using Illumina GAIIx. 4C sequencing analysis in espohageal adenocarcinoma cell line.

2020-06-14 | GSE132813 | GEO

Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma [ChIP-Seq]

2019-07-30 | GSE132680 | GEO

Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma [4C-Seq]

Project description:We report the application of circular chromatin conformation capture (4C) sequencing technology for master transcription factor (KLF5 and ELF3) in human esophageal adenocarcinoma cancer cell lines (ESO26) . By baiting the promoters of KLF5 and ELF3, we esatblished the interaction with unknown enhnacer marks. Overall design: 4C sequencing analysis of espohageal adenocarcinoma cell line

2019-07-30 | GSE132685 | GEO

Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in esophageal adenocarcinoma

Project description:This SuperSeries is composed of the SubSeries listed below. Overall design: Refer to individual Series

2019-07-30 | GSE132686 | GEO

Core transcriptional regulatory circuitry in human hepatocytes.

Project description:We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that these regulators form a highly interconnected core circuitry, and reveal the local regulatory network motifs created by regulator-gene interactions. Autoregulation was a prominent theme among these regulators. We found that hepatocyte master regulators tend to bind promoter regions combinatorially and that the number of transcription factors bound to a promoter corresponds with observed gene expression. Our studies reveal portions of the core circuitry of human hepatocytes.

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Chromatin immunoprecipitation analysis of human hepatocyte regulatory circuitry

Project description:We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that these regulators form a highly interconnected core circuitry, and reveal the local regulatory network motifs created by regulator-gene interactions. Auto-regulation was a prominent theme among these regulators. We found that hepatocyte master regulators tend to bind promoter regions combinatorially and that the number of transcription factors bound to a promoter corresponds with observed gene expression. Our studies reveal portions of the core circuitry of human hepatocytes.

2006-05-09 | E-WMIT-9 | BioStudies

Chromatin immunoprecipitation analysis of human hepatocyte regulatory circuitry

Project description:We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that these regulators form a highly interconnected core circuitry, and reveal the local regulatory network motifs created by regulator-gene interactions. Auto-regulation was a prominent theme among these regulators. We found that hepatocyte master regulators tend to bind promoter regions combinatorially and that the number of transcription factors bound to a promoter corresponds with observed gene expression. Our studies reveal portions of the core circuitry of human hepatocytes.

2006-05-09 | E-WMIT-9 | ArrayExpress

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