|
| Status |
Public on Apr 17, 2014 |
| Title |
4-LNCaP-Hes6-Bic-E2F1-ChIP |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
antibody: E2F1(C-20)
vendor: SantaCruz
catalog#: sc-193
condition: overexpressing Hes6 and Bicalutamide treated
|
| Treatment protocol |
Bicalutamide 1uM or Vehicle (Ethanol)
|
| Growth protocol |
RPMI & 10% Foetal Bovine Serum & Puromycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) 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 DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Alignments: Sequences generated by the Illumina Genome Analyzer were processed by the Illumina analysis pipeline version 1.6.1, and aligned to the Human Reference Genome (assembly hg18, NCBI Build36.1, March 2008) using BWA version 0.5.523.
Reads were filtered by removing those with a BWA alignment quality score less than 15.
Peaks: Enriched regions of the genome were identified by comparing the ChIP samples to input samples using the MACS peak caller version 1.3.7.113.
Genome_build: hg18
Supplementary_files_format_and_content: wig files
|
| |
|
| Submission date |
Mar 19, 2012 |
| Last update date |
Apr 17, 2014 |
| Contact name |
Roslin Russell |
| E-mail(s) |
roslin.russell@cruk.cam.ac.uk
|
| Phone |
01223 769770
|
| Organization name |
Cambridge Research Institute, Cancer Research UK
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE36526 |
Hes6 drives a network with therapeutic potential in castrate-resistant prostate cancer |
| GSE36614 |
Hes6 expression is controlled by c-Myc and the AR to promote E2F1 activity and poor outcome in castrate-resistant prostate cancer (E2F1 ChIP-seq) |
|
| Relations |
| BioSample |
SAMN02197607 |
