|
| Status |
Public on Oct 05, 2016 |
| Title |
ChIPseq_LNCaP_FOXA1_TNFa_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
treatment 1: TNF-alpha (1000 U/ml, 2h)
treatment 2: -
antibody: anti-FOXA1 (Abcam, ab23738)
|
| Treatment protocol |
Cells were maintained in RPMI 1640 medium with 10% charcoal-stripped for two days to deplete androgens actions and then exposed to vehicle (DMSO), DHT (100 nM 5a-dihydrotestosterone), TNF-alpha (1000 U/ml), or DHT and TNF-alpha for two hours. FOXA1 silencing was done by reverse-transfecting LNCaP cells with siRNAs against FOXA1 or control siRNA (Dharmacon; On-TARGETplus pool or non-targeting pool) with Lipofectamine RNAiMAX transfection reagent. Experiments were performed four days after transfection.
|
| Growth protocol |
LNCaP cells (from ATCC) were grown in RPMI1640 (Gibco) supplemented with 10 % fetal bovine serum, 1 % penicillin/streptomycin, and 2 mM l-glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei from approximately 10 million formaldehyde crosslinked (1%; 10min at room temperature) cells were isolated and chromatin was fragmented using sonicator (bioruptor). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and protein-A magnetic beads. DNA fragments were purified and libraries were prepared according to standard Illumina protocol. Samples were sequenced at GeneCore in EMBL (Heidelberg, Germany).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
Reads were aligned against human genome hg19 with Bowtie software (0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19.
Peak calling was done using findPeaks tool of HOMER software (V 4.7.2; http://homer.salk.edu/homer/) with default parameters and chromatin input sample as a control . Bed files were done using pos2bed.pl tool.
BedGraph files were done using HOMER software (V 4.7.2; http://homer.salk.edu/homer/) by combining two replicates and normalizing total number of reads to 10 million. GROseq signal is divided between plus- and minus-strand signals in separate files.
Genome_build: hg19
Supplementary_files_format_and_content: Common binding sites of two biological replicates as bed files are provided for ChIP-seq samples where peaks were detected. Signal intensities as tdf files are provided for GRO-seq data (minus and plus-strand signals in separate files) and ChIP-seq samples for which the peak detection was not reliable due to low signal enrichment (androgen receptor in DMSO and TNF-alpha; p65 in DMSO and DHT).
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Einari A Niskanen |
| E-mail(s) |
einari.niskanen@uef.fi
|
| Organization name |
University of Eastern Finland
|
| Department |
School of Medicine
|
| Lab |
Biomedicine
|
| Street address |
Yliopistonranta 8
|
| City |
Kuopio |
| ZIP/Postal code |
70210 |
| Country |
Finland |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE83860 |
Crosstalk between androgen and proinflammatory signaling activates a distinct transcription program in prostate cancer cells |
|
| Relations |
| BioSample |
SAMN05327772 |
| SRA |
SRX1885187 |
