|
| Status |
Public on Jun 13, 2013 |
| Title |
LNCaP-H3K4me1 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: prostate cancer
chip antibody: Rabbit Anti-Histone monomethyl-H3 (Abcam ab8895, Lot GR61280-1)
treatment: None
|
| Growth protocol |
LNCaP cells were grown in 10% FBS. For baseline ChIP-Seq (ETV1 and H3K4me1 ChIP), 100 million and 20 million cells were harvested respectively. For ETV1 and scrambled knockdown experiments, 25 million cells were infected with lentiviral shRNA at MOI~5 and cells were harvested 72 hours later.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked for 15-minutes in 1% parformaldehyde. Cells were lysed and chromatin sheared using bioruptor. Sheared chromatin was incubated with anti-rabbit IgG dynabeads pre-conjugated with 5 ug of the indicated antibody, washed, eluted, reverse cross-linked, and purified.
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 18 cycles. DNA was purified using Ampure beads and 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 IIx |
| |
|
| Description |
LNCaP Cells (25 million), H3K4me1 ChIP-Seq.
|
| Data processing |
All reads (36-bp) from ChIP-Seq were aligned to the human genome (build 36, or hg18) using the ELAND alignment software within the Illumina Analysis Pipeline.
Replicate reads were removed and counted as one
Peaks were called using MACS 1.4 comparing with input DNA of LNCaP cells
Genome_build: hg18
Supplementary_files_format_and_content: BED files, containing genomic coordinates of peaks
|
| |
|
| Submission date |
May 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
|
| Phone |
646-888-3356
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Chen
|
| Street address |
1275 York Ave, Box 20
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE47120 |
Effect of ETV1 knockdown on genome wide AR binding in LNCaP Cells |
| GSE47220 |
ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss |
|
| Relations |
| BioSample |
SAMN02147287 |
| SRA |
SRX283755 |
