|
| Status |
Public on Sep 05, 2017 |
| Title |
HOXB13_veh_repl1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Prostate cancer cell line LNCaP
procedure: Chromatin IP against HOXB13
chip antibody: HOXB13 (sc-66923; Santa Cruz)
|
| Treatment protocol |
Cells were treated with 10nM R1881 or vehicle for 4 hours.
|
| Growth protocol |
LNCaP cells were cultured in RPMI-1640 supplemented with 10% FBS. Cells were hormone deprived three days before R1881 stimulation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Embo Mol Med 2015) For each ChIP, 5-10μg of antibody prebound to protein A or protein G beads was used.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Kapa Biosystems kit,KK8234).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequences were generated by the Illumina Hiseq 2500 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-5. DFilter was run with bs=50, ks=30, refine, nonzero.
Genome_build: hg19
|
| |
|
| Submission date |
Feb 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Suzan Stelloo |
| E-mail(s) |
Stelloo@science.ru.nl
|
| Organization name |
Radboud University
|
| Department |
Molecular Biology
|
| Street address |
Geert Grooteplein Zuid 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE94682 |
Endogenous Androgen Receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis |
|
| Relations |
| BioSample |
SAMN06312210 |
| SRA |
SRX2545053 |
