GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2463797 Query DataSets for GSM2463797
Status Public on Jul 18, 2017
Title R1881_mTOR_ChIP-seq.bam.bigwig
Sample type SRA
Source name LNCaP human prostate cancer cell line treated with R1881 for 48h
Organism Homo sapiens
Characteristics cell line: LNCaP prostate tumor cell line
treatment: R1881
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
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
BioSample SAMN06242171
SRA SRX2505194

Supplementary file Size Download File type/resource
GSM2463797_R1881_mTOR_ChIP-seq.ucsc.bedGraph.gz 52.0 Mb (ftp)(http) BEDGRAPH
GSM2463797_mTOR_peaks_R1881.csv.gz 10.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap