|
| Status |
Public on Jan 13, 2016 |
| Title |
siControl FoxA1 ChIP-seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP-abl siControl
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer cells
passages: 62-64
cell line: LNCaP-abl
chip antibody: FoxA1 (Abcam ab23738)
|
| 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 |
genomic DNA |
| 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 |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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: bigwig
|
| |
|
| Submission date |
Sep 09, 2015 |
| 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 |
SAMN04043896 |
| SRA |
SRX1212232 |
