|
| Status |
Public on Mar 09, 2010 |
| Title |
H3K4me2_DHT_16h_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP prostate cancer cell line
cell type: prostate cancer Cells
passages: 14-17
agent: DHT
time: 16h
chip antibody: anti-H3K4me2
|
| Treatment protocol |
Cells were cultured in RPMI 1640 supplemented with 10% charcoal-stripe FBS for 4 days, and then treated with DHT or Ethanol for 4 or 16 hours
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from MNase digested chromatin 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 18 cycles and library fragments of ~220 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 |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3K4me2. Mono-nucleosome level histone mark ChIP-Seq data (Mnase ChIP).
|
| Data processing |
Bed: Sequence reads were obtained and mapped to the human genome (March, 2006) using the Illumina Genome Analyzer Pipeline.
Peaks: Peak detection was performed with the "Nucleosome Positioning from Sequencing (NPS)" algorithm (http://liulab.dfci.harvard.edu/NPS/)
Processed data file build: hg18
|
| |
|
| Submission date |
Feb 01, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Housheng Hansen He |
| E-mail(s) |
housheng@jimmy.harvard.edu
|
| Phone |
617-632-4738
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Myles Brown
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE20042 |
Genome-wide maps of H3K4me2/3 in prostate cancer cell line LNCaP |
|
| Relations |
| SRA |
SRX017345 |
| BioSample |
SAMN00009601 |
| Named Annotation |
GSM503905_LNCaP_H3K4me2_DHT_16h.bed.gz |
