 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 15, 2020 |
| Title |
SREBF1 coordinates with master transcription factors in regulating lipid metabolism and cancer-promoting pathways in squamous cell carcinoma |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We 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 factor (SREBF1) in human ESCC cancer cell lines (TE5).
|
| |
|
| Overall design |
Esophageal Squamous cell carcinomas cell lines were harvested, and ChIPseq was performed using transcription factor antibodies. KYSE150 and TE5 cells knock-down SREBF1 with siRNA and negative control were generated by deep sequencing, using Illumina GAIIx. 4C sequencing analysis in espohageal squamous cell carcinomas cell line.
|
| |
|
| Contributor(s) |
Li L, Yang Q, Jiang Y, Yang W, Jiang Y, Hazawa M, Zhou B, Li X, Gery S, Ding L, Ho AS, Zumsteg ZS, Wang M, Ding Y, Freedland SJ, Xu L, Li E, Koeffler HP, Lin D |
| Citation(s) |
34272396 |
| |
| Submission date |
Jan 16, 2020 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Qian Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
CEDARS SINAI MEDICAL CENTER
|
| Department |
Department of Surgery
|
| Lab |
Michael R Freeman
|
| Street address |
8700 Beverly Blvd
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90048 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL22790 |
Illumina MiniSeq (Homo sapiens) |
|
| Samples (13)
|
|
| Relations |
| BioProject |
PRJNA601742 |
| SRA |
SRP242234 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143803_KYSE150_siSREBF1_readCounts_genes.txt.gz |
309.2 Kb |
(ftp)(http) |
TXT |
| GSE143803_RAW.tar |
907.9 Mb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
| GSE143803_TE5_siSREBF1_readCounts_genes.txt.gz |
243.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...