|
| Status |
Public on Jun 02, 2014 |
| Title |
AR_ChIP-seq_shFoxA1_hormone-deprived |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
genotype/variation: FoxA1 knockdown
chip antibody: anti-AR
chip antibody vendor: Millipore
chip antibody catalog#: 06-680
chip antibody lot#: JBC1860890
treatment protocol: hormone-deprived
|
| 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 lines were maintained in RPMI supplemented with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
Chromatin IP against AR
|
| Data processing |
Reads were aligned to the reference genome using Eland software (Illumina)
Peak-calling by HOMER v3.8
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 |
Apr 27, 2012 |
| 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 |
| SRA |
SRX147605 |
| BioSample |
SAMN00990228 |
