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| Status |
Public on Jun 14, 2020 |
| Title |
Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
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| Summary |
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).
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| 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.
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| Contributor(s) |
Pan J, Silva TC, Gull N, Yang Q, Plummer J, Chen S, Daigo K, Hamakubo T, Ding L, Klempner SJ, Berman BP, Koeffler HP, Lin D |
| Citation(s) |
32332020 |
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| Submission date |
Jun 17, 2019 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Qian Yang |
| E-mail(s) |
qian.yang@cshs.org
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| Organization name |
CEDARS SINAI MEDICAL CENTER
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| Department |
Department of Surgery
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| Lab |
Michael R Freeman
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| Street address |
8700 Beverly Blvd
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
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| Platforms (3) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL22790 |
Illumina MiniSeq (Homo sapiens) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA549160 |
| SRA |
SRP201581 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE132813_ESO26_HNF4A_RNA-seq_normalized_count.txt.gz |
713.1 Kb |
(ftp)(http) |
TXT |
| GSE132813_RAW.tar |
4.6 Mb |
(http)(custom) |
TAR (of BIGWIG, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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