|
| Status |
Public on Jun 30, 2020 |
| Title |
ChIP-seq of MYC 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: MYC (ab32072, Abcam)
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 MYC 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 |
A2-167-3
|
| 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
Peaks were scaled using the trimmed mean of M-values.
Peaks were scaled to Drosophila Dm6 spike-in controls.
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 |
SRX6717237 |
| BioSample |
SAMN12574708 |
