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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: PRJNA548754 | ENA |

REPOSITORIES: ENA

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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]

Project description: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 [ChIP-Seq]

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.

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.

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.

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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.

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A Transcriptional Regulatory Loop of Master Regulator Transcription Factors, PPARG, and Fatty Acid Synthesis Promotes Esophageal Adenocarcinoma

Project description:We profiled esophageal adenocarcinoma 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, RNA-Seq, 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 or OE33 cells knock down PPARG 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 ChIP sequencing technology for studying master transcription factor (PPARG) in human esophageal adenocarcinoma cancer cell lines (Eso26 and OE33).

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Distal regulation mediated Core Transcriptional Regulatory Circuitry in Esophageal Squamous Cell Carcinoma

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Chemicals orchestrate reprogramming with hierarchical activation of master transcription factors primed by endogenous Sox17 activation

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