|
| Status |
Public on Jul 18, 2017 |
| Title |
Control_mTOR_ChIP-seq.bam.bigwig |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP human prostate cancer cell line treated with vehicle for 48h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP prostate tumor cell line
treatment: control
chip antibody: mTOR
|
| Treatment protocol |
Cells were treated for 48h with R1881 (10nM) or vehicle (EtOH).
|
| Growth protocol |
LNCaP cells were seeded in RPMI media with no phenol red and with charcoal-stripped serum (no steroids) . 48h later, cell were treated with 10nM R1881 or vehicle (EtOH) for 48h before crosslink.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 48h treatment with vehicle or R1881 nuclei were isolated and subjected to chromatin immunoprecipitation. Following mTOR ChIP, genomic DNA was purified with QIAGEN DNA extraction kit.
Libraries were performed at the Génome Québec Innovation Centre (McGill University) using standard protocol for HiSeq - Illumina Single reads 50bp sequencing lane
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
genomic DNA enriched following mTOR chromatin immunoprecipitation
|
| Data processing |
Sequences were aligned to the human genome database (Hg19) using BWA v0.5.9 (Li and Durbin, 2009)
Significant DNA binding (peak) was determined using MACS v1.4.1 software (Zhang et al., 2008).
Peak annotation, tag directory, bed file generation, and de novo motif discovery were performed with the Homer package v3.18.
Genome_build: hg19
Supplementary_files_format_and_content: data are presented as BedGraph and annotated peak lists in excel from the merged of two samples for control condition and two samples for R1881-treated cells.
|
| |
|
| Submission date |
Jan 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Etienne Audet-Walsh |
| E-mail(s) |
etienne.audet-walsh@crchudequebec.ulaval.ca
|
| Organization name |
Université Laval
|
| Department |
Molecular Medicine
|
| Street address |
2705 boulevard Laurier
|
| City |
Québec City |
| State/province |
QC |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE93845 |
Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer progression [ChIP-seq] |
| GSE93846 |
Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer progression |
|
| Relations |
| BioSample |
SAMN06242172 |
| SRA |
SRX2505193 |
