NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE97831 Query DataSets for GSE97831
Status Public on Feb 07, 2018
Title RNA-seq and ChIP-seq analysis of BMI1 or RING1B-silenced prostate cancer cells C4-2
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: Study of the role of BMI1 dependent and indpendent of PRC1 in castration-resistant prostate cancer(CRPC) Method: The expression of BMI1 or RING1B was silenced by 2 independent siRNA strands targeted at BMI1 or RING1B in C4-2 cells, scramble RNA as control. mRNA profiles and genome-wide chromatin-state maps were generated by deep sequencing. AR, BMI1 and IgG ChIP was conducted in C4-2 cells. Results: AR-induced genes were significantly down regulated by BMI1 knockdown but not RING1B. higher expression levels of BMI1 activated genes (those downregulated by BMI1 knockdown) were significantly associated with poorer disease-free and poorer overall survival.
 
Overall design Expression profiling by RNA-seq, profiling of BMI1 and RNF2 (wildtype and knockdown) from C4-2 cell lines. DNA was purified from chromatin immunoprecipitates for AR, BMI1 or IgG using the phenol/chloroform extraction. IgG was used as a negative control for ChIP. Then, DNA was amplified by quantitative PCR and normalized to input.
 
Contributor(s) Zhu S, Zhao D, Chen K, Cao Q
Citation(s) 29402932
Submission date Apr 14, 2017
Last update date May 15, 2019
Contact name Dongyu Zhao
E-mail(s) zhaodyemail@gmail.com
Organization name Houston Methodist Research Institute
Street address 6670 Bertner Ave
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (9)
GSM2579115 Control_RNAseq_Rep1
GSM2579116 Control_RNAseq_Rep2
GSM2579117 BMI1_Knockdown_RNAseq_Rep1
Relations
BioProject PRJNA382981
SRA SRP103945

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE97831_RAW.tar 146.8 Mb (http)(custom) TAR (of WIG)
GSE97831_genes_expression_table.txt.gz 651.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap