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Series GSE63034 Query DataSets for GSE63034
Status Public on Jan 13, 2016
Title Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
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 work is comprehensive analysis of target genes co-regulated by CREB1 and FoxA1 in prostate cancer cell models, tissues, and circulating tumor cells (CTCs). Expression of CREB1/FoxA1 target genes corresponds with disease recurrence and aggressive clinical features.
Methods: LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. For RNA-seq, cells are transfected with FoxA1,CREB1 specific or nonspecific siRNA and total RNA is extracted with Qiangen RNeasy Mini kit(cat 74104) and library is generated with TruSeq RNA Sample Preparation Kit v2 from Illumina(cat RS-122-2001). For Chip-seq, LNCaP cells between passage number 32-34 and abl between 62-64 were used for assay. After crosslinking with 1% formaldehyde, 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.

Overall design LNCaP cells and LNCaP cells were used as cell model. Library was sequenced using Illumina HISeq 2500.
Contributor(s) Wu D, Liu X, Ye Z, Sunkel BD, Wang Q
Citation(s) 26743006
Submission date Nov 06, 2014
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 (17)
GSM1538429 abl_CREB1 ChIP-seq
GSM1538430 abl_FOXA1 ChIP-seq
GSM1538431 LNCaP_CREB1 ChIP-seq
BioProject PRJNA266510
SRA SRP049591

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
GSE63034_ABL-SIC.readcount.txt.gz 128.0 Kb (ftp)(http) TXT
GSE63034_ABL-siCREB1.readcount.txt.gz 191.9 Kb (ftp)(http) TXT
GSE63034_ABL-siFOXA1.readcount.txt.gz 191.8 Kb (ftp)(http) TXT
GSE63034_LNCaP-SIC.readcount.txt.gz 129.4 Kb (ftp)(http) TXT
GSE63034_LNCaP-siCREB1.readcount.txt.gz 194.8 Kb (ftp)(http) TXT
GSE63034_LNCaP-siFOXA1.readcount.txt.gz 194.2 Kb (ftp)(http) TXT
GSE63034_RAW.tar 3.1 Gb (http)(custom) TAR (of BED, BW, TXT, WIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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