|
| Status |
Public on Apr 04, 2016 |
| Title |
LNCaP_H3K27ac_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer cells LNCaP
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
cell line: LNCaP
chip-antibody: H3K27Ac (#39297, Active Motif)
|
| Growth protocol |
Cell lines were cultured according to manufacturer's instructions
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were purified after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP.
Libraries for ChIP-Seq were prepared following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to hg19 using bowtie v0.12.8 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
Broad peaks were called with Peak Ranger version 1.16 with parameters ccat: format: bam, read extension length: 200, FDR cut off: 0.11, sliding window size: 500, window moving step: 50, min window reads: 4 and min window fold change: 5.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using Peak Ranger version 1.16
|
| |
|
| Submission date |
Oct 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Joanna Achinger-Kawecka |
| E-mail(s) |
j.achinger@garvan.org.au
|
| Organization name |
Garvan Institute of Medical Research
|
| Street address |
384 Victoria Street
|
| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE73783 |
Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [ChIP-seq] |
| GSE73785 |
Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations |
|
| Relations |
| BioSample |
SAMN04147551 |
| SRA |
SRX1308544 |
