|
| Status |
Public on Jul 25, 2017 |
| Title |
CPCG_0365_H3K27ac ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
primary prostate cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary prostate cancer
antibody: H3K27ac (Abcam cat. ab4729)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted following sonication, clearing of lysates, and immunoprecipitation of protein/DNA complexes.
Libraries were constructed using Rubicon Thruplex FD kit using manufacturer's recommended protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
The raw data cannot be stored with GEO due to patient privacy and has instead been uploaded to the European Genome/Phenome Archive (EGAS00001002496)
|
| Data processing |
Bowtie 2 was used to align reads to the reference Hg19 genome.
MACS2 was used to call peaks using a q-value threshold of less than or equal to 0.005
Bedgraph files were generated using HOMER v4.7 with the makeUCSCfile command
Genome_build: hg19
Supplementary_files_format_and_content: Bed files correspond to the called peaks files from MACS2 after aligning to hg19 using Bowtie 2
|
| |
|
| Submission date |
Jul 05, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Ken Kron |
| Organization name |
University Health Network
|
| Street address |
101 College Street, TMDT, 11th floor, room 11-601B
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE96652 |
Genomic profiling of H3K27ac and transcription factor binding in ERG-overexpressing prostate cancer |
|
| Relations |
| BioSample |
SAMN07315482 |
