|
| Status |
Public on Jun 02, 2014 |
| Title |
FAIRE_DU145 AR + FoxA1 high |
| Sample type |
SRA |
| |
|
| Source name |
FAIRE_DU145 AR + FoxA1 high
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: prostate cancer cell line DU145
ectopic expression: AR wildtype + FoxA1 high
chip antibody: N/A
|
| Treatment protocol |
DU145 AR cells were infected with LacZ or FOXA1 adenovirus for 48 hours to overexpress FOXA1 protein prior to collect cell pellets for ChIP or FAIRE experiments
|
| Growth protocol |
DU145 cells were routinely maintained in RPMI supplemented with 10% FBS plus 1% antibiotics (penicillin and streptomycin)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Antibodies were from abcam (cat#ab23738,GR77830-1) and Millipore (cat#06-680, lot#JBC1939961) and ChIP was performed using 5e6-10e6 cells per reaction. Chromatin was fixed in room temperature for 10 minutes with serum free media containing 0,37 % formaldehyde. Cells were washed twice in PBS and scraped before treatment of cell lysis buffer with protease inhibitors on ice. Pelleted nuclei were sheared to 200-700bp using an ultrasonic sonicator (Misonix). ChIP was done with 5 micrograms of antibody. FAIRE analysis was performed according to the protocol published by Giresi et al .
Libraries were prepared according to Bioo Scientific's instructions accompanying the DNA Sample Kit (Part# 514101). 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 (3' to 5' 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 Illumina HiSeq 2000 or Illumina HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FAIRE-seq
m100
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bwa version 0.61
Peak-calling by HOMER v4.1
Genome_build: hg19
Supplementary_files_format_and_content: Columns in peaks.txt contain information about each peak: Column 1: PeakID - a unique name for each peak. Column 2: chr - chromosome where peak is located. Column 3: starting position of peak. Column 4: ending position of peak. Column 5: Strand (+/-). Column 6: Normalized Tag Counts - number of tags found at the peak, normalized to 10 million total mapped tags (or defined by the user). Column 7: Focus Ratio - fraction of tags found appropriately upstream and downstream of the peak center (see below). Column 8: Peak score (position adjusted reads from initial peak region - reads per position may be limited). Columns 9+: Statistics and Data from filtering.
|
| |
|
| Submission date |
Jun 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong-Jian Jin |
| E-mail(s) |
hongjian-jin@northwestern.edu
|
| Phone |
3125033041
|
| Organization name |
Northwestern University
|
| Department |
Medicine
|
| Street address |
303 E Superior St
|
| City |
Chicago |
| State/province |
IL - Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE47987 |
FoxA1 inhibits androgen receptor expression and suppresses prostate cancer metastasis [DU145, ChIP-seq] |
| GSE55007 |
Cooperativity and Equilibrium with FOXA1 Define Androgen Receptor Transcriptional Program |
|
| Relations |
| BioSample |
SAMN02204356 |
| SRA |
SRX306522 |
