GSE143803 SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma

Contributors : Liyan Li ; Qian Yang ; Yanyi Jiang ; Wei Yang ; Yuan Jiang ; Masaharu Hazawa ; Bo Zhou ; Xiang Li ; Sigal Gery ; Lingwen Ding ; Allen S Ho ; Zachary S Zumsteg ; Mingrong Wang ; Yanbing Ding ; Stephen J Freedland ; Liyan Xu ; Enmin Li ; H P Koeffler ; Dechen LinSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe profiled esophageal squamous cell carcinorma (ESCC) 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 ESCC cells knock down SREBF1 with siRNA and negative 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 ...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research