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Sample GSM941211 Query DataSets for GSM941211
Status Public on Jun 01, 2015
Title LNCaP-SiGATA2-REP2
Sample type SRA
 
Source name LNCaP-SiGATA2
Organism Homo sapiens
Characteristics cell line: LNCaP
cell type: prostate cancer cells
treated with: siGATA2
passages: 32-34
Treatment protocol 4 days before ChIP assay, the full medium was changed to RPMI medium supplied with 5% charcal treated FBS without anti-biotics.
Growth protocol LNCaP cells were routinely cutured in RPMI medium supplemented with 10% FBS.
Extracted molecule total RNA
Extraction protocol RNA mRNA was isolated with Rneasy Mini kit from Qiagen. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample KitPart # 15008136. Briefly, the polyA containing mRNA was purified, fragmented, and reverse transcribed. This was followed by second strand cDNA synthesis. The cDNA fragments went through end repair, adapter ligation, and PCR amplification processes. The final cDNA library was sequenced by Illumina HiSeq2000 in OSUCCC sequencing core.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 4
Data processing Sequenced reads were mapped to hg19 by TopHat, and those uniquely mapped reads were used for further analysis.
Differentially expressed genes are retrived by edgeR software with p<0.001.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed gene list from edgeR output
 
Submission date Jun 01, 2012
Last update date May 15, 2019
Contact name Zhenqing Ye
E-mail(s) yez@uthscsa.edu
Organization name The University of Texas Health Science Center at San Antonio
Department Department of Molecular Medicine
Street address 7703 Floyd Curl Drive
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL11154
Series (2)
GSE38393 Hi-seq 2000 sequencing facilitates quantitative analysis of transcriptomes in LNCaP cells with or without SiGATA2 treatment.
GSE38452 A Class of H3K4me1/H3K9me2 marked active GATA2 enhancers directs a GATA2-dependent transcription program underlying prostate cancer progression.
Relations
SRA SRX150916
BioSample SAMN01001651

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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