|
| Status |
Public on Jun 02, 2014 |
| Title |
AR_ChIP-seq_shCtrl_R1881, biological replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
genotype/variation: control
chip antibody: anti-AR
chip antibody vendor: Millipore
chip antibody catalog#: 06-680
chip antibody lot#: JBC1939961
|
| Treatment protocol |
Chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using an ultrasonic sonicator (Misonix), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
|
| Growth protocol |
LNCaP cellss were maintained in RPMI supplemented with 10% FBS.
|
| 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 HiScan following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Chromatin IP against AR
|
| 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 The bedGraph format is described http://genome.ucsc.edu/goldenPath/help/bedgraph.html
|
| |
|
| Submission date |
Feb 13, 2014 |
| 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 |
GPL15456 |
| Series (2) |
| GSE37345 |
FoxA1 inhibits androgen receptor expression and suppresses prostate cancer metastasis [LNCaP, ChIP-seq] |
| GSE55007 |
Cooperativity and Equilibrium with FOXA1 Define Androgen Receptor Transcriptional Program |
|
| Relations |
| BioSample |
SAMN02641795 |
| SRA |
SRX470407 |
