|
| Status |
Public on Mar 25, 2012 |
| Title |
LNCaP DHT DNaseI |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer cells
passages: 14-17
treatment: DHT
sample type: DNase-seq
|
| Treatment protocol |
Cells were cultured in RPMI 1640 supplemented with 10% charcoal-stripe FBS for 3 days, and then treated with DHT or Ethanol for 4 hours for prostate cancer cells, treated with E2 or Ethanal for 45mins for breast cancer cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H3K4me2 ChIPed DNA or the size selected DNase I digested DNA was used for library preparation. 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 (for H3K4me2 ChIP-seq) or 200~300bp (for DNase-seq) (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 or HiSeq machine following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
DNase-seq
|
| Data processing |
bed: Sequence reads were obtained and mapped to the human (March, 2006) genomes
|
| |
|
| Submission date |
Oct 25, 2011 |
| 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) |
| GSE33216 |
Genome-wide maps of H3K4me2 and DNase I hypersensitivity sites in prostate cancer cell line LNCaP and breast cancer cell line MCF-7. |
|
| Relations |
| SRA |
SRX103260 |
| BioSample |
SAMN00744396 |
| Named Annotation |
GSM822388_lncap_dht_dnasei_new.bed.gz |
