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| Status |
Public on Jan 21, 2014 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of effect of knockdown of GATA2 on AR binding sites |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare AR binding activity in LNCaP cells with and without knockdown of GATA2.
Methods: LNCaP cells between passage number 32-34 were used for assay. Cells are transfected with GATA2 specific or nonspecific siRNA and ChIP was performed, the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks.
Results: GATA2 knockdown lead to changes of AR binding activity , in most AR binding sites, AR shows decreased bindig activity. Only small percent sites show increased binding.
Conclusions: Our study represents the first detailed analysis of the relationship between GATA2 and AR binding in whole genomic DNA.These results demostrate GATA2 play a critical role in AR activity in prostate cancer.
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| Overall design |
LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.
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| Contributor(s) |
Wu D, Liu X, Wang Q |
| Citation(s) |
24423874 |
| Submission date |
Nov 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Qianben Wang |
| E-mail(s) |
Qianben.Wang@osumc.edu
|
| Phone |
6142471609
|
| Organization name |
Ohio State University
|
| Department |
Molecular and Cellular Biochemistry and the Comprehensive Cancer Center
|
| Street address |
460 W 12th Avenue
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA229904 |
| SRA |
SRP033312 |
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