|
| Status |
Public on Jun 30, 2020 |
| Title |
ChIP-seq of H3K27ac in LNCaP/MYC KD 512 Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
condition: MYC Knockdown Construct 512
chip antibody: H3K27ac (39133, Active Motif)
replicate: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked chromatin was extracted from cells using the Active Motif ChIP-it kit
Cells were crosslinked and lysed, and chromatin was sheared to 200-1000bp. 30 micrograms of chromatin were incubated with H3K27ac antibody overnight, immunoprecipiated, and DNA was purified using the Active Motif ChIP-IT High Sensitivity Kit. DNA was constructed into libraries using the Illumina TruSeq ChIP Library Preparation Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
A2-167-13
|
| Data processing |
Libraries were sequenced 76 cycles single-end.
FASTQ files were adaptor trimmed using TrimGalore, aligned with BWA to b37, and sorted using PICARD.
Read pileups were summarized into bigwig files using DeepTools
Genome_build: b37
Supplementary_files_format_and_content: bigwig format of sequence read pileups
|
| |
|
| Submission date |
Aug 18, 2019 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Adam Sowalsky |
| Organization name |
National Cancer Institute
|
| Department |
LGCP
|
| Lab |
Sowalsky Lab
|
| Street address |
37 Convent Drive Building 37 Room 1062B
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE135942 |
Genetic studies of MYC in prostate cancer cell lines |
|
| Relations |
| SRA |
SRX6717273 |
| BioSample |
SAMN12574708 |
