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Series GSE52725 Query DataSets for GSE52725
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
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.
Overall design LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.
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
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
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM1274871 siControl-AR_ChIP Seq
GSM1274872 siGATA2-AR_ChIP Seq
GSM1274873 FoxA1_ChIP Seq
BioProject PRJNA229904
SRA SRP033312

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Supplementary file Size Download File type/resource
GSE52725_RAW.tar 1.7 Gb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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