|
| Status |
Public on Apr 01, 2017 |
| Title |
GRHL2_ChIP-seq_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP_anti-GRHL2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
chip antibody: Sigma HPA004820
|
| Growth protocol |
LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
LNCaP cells were seeded at 3x10^6 cells/plate in 15cm plates in RMPI 1640 + 10% FBS and allowed to grow for 3 days prior to fixation with formaldehyde. Nuclear pellets were sonicated on ice for 10 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor. Lysates were immunoprecipitated with 4 ug GRHL2 antibody (Sigma HPA004820) or 5 ug AR antibody (Santa Cruz sc-816 X), which had been pre-coupled to Protein G Dynabeads (Life Technologies, 10004D). DNA was purified using a PCR purification kit (Qiagen) and eluted in 100 µl.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed in BaseSpace
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, with default parameters.
Reads were filtered using minimum MAPQ quality score of 15.
Peaks were called using MACS with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated in Galaxy
|
| |
|
| Submission date |
Apr 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Luke Selth |
| E-mail(s) |
luke.selth@flinders.edu.au
|
| Organization name |
Flinders University
|
| Department |
College of Medicine and Public Health
|
| Street address |
Flinders Drive
|
| City |
Bedford Park |
| State/province |
SA |
| ZIP/Postal code |
5042 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE80256 |
Grainyhead-like 2 is essential for androgen receptor expression and activity in prostate cancer (ChIP-seq) |
| GSE80452 |
Grainyhead-like 2 is essential for androgen receptor expression and activity in prostate cancer |
|
| Relations |
| BioSample |
SAMN04851078 |
| SRA |
SRX1703571 |
