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Sample GSM1538434 Query DataSets for GSM1538434
Status Public on Jan 13, 2016
Title abl-siFoxA1 RNA-seq
Sample type SRA
 
Source name abl-siFoxA1 RNA-seq
Organism Homo sapiens
Characteristics cell line: LNCaP-abl
passage number: 62-64
group: androgen independent
transfection: siFoxA1
Treatment protocol LNCaP or LNCaP-abl cellswere treated with 40nM siControl or siFoxA1,SiCREB1 from Dharmacon company for 3 days.
Growth protocol LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium when treatment are performed.LNCaP abl cells were cultured in 10% charcoal stripped FBS in RPMI 1640 medium, 1:2 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium when treatment are performed.
Extracted molecule total RNA
Extraction protocol For RNA, follow protocol in Rneasy Mini Kit. For Chip-seq, lysates were clarified from sonicated nuclei and CREB1-DNA complexes were isolated with corresponing antibody.
For ChIP-seq libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.For RNA-seq, follow instruction for TruSeq RNA Sample Preparation Kit v2 from Illumina(cat RS-122-2001).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Prostate cancer derived cell lines
Data processing Basecalls were performed using CASAVA version 1.8.
RNA-seq reads were aligned to the hg19 genome assembly using tophat-2.0.8 (Bowtie2-2.1.0) with default parameters and UCSC refGene annotation file. Mapped reads with multiple accepted alignments were removed using a Perl program.
HTSeq-0.5.3p9 was used to count the uniquely mapped reads in union mode.
Genes with differential expressions were detected using edgeR_3.0.6 with FDR threshold 0.05.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0 with parameters '-k 2 -v 2' to report up to two valid alignments. Mapped reads with two valid alignments were removed using a Perl program. Uniquely mapped reads from replicates of the same sample were pooled.
Peaks were called using MACS v1.4.2 with parameters '-m 3,30 -g hs -p 1e-8'.
Genome_build: hg19
Supplementary_files_format_and_content: wig, txt
 
Submission date Nov 06, 2014
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
 
Platform ID GPL16791
Series (1)
GSE63034 Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence
Relations
BioSample SAMN03165739
SRA SRX752912

Supplementary file Size Download File type/resource
GSM1538434_ABL-siFOXA1_edger.05.txt.gz 336.3 Kb (ftp)(http) TXT
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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