|
| Status |
Public on Jan 31, 2013 |
| Title |
RNAP2_NT_BR2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP prostate cancer cells
treatment: nontreated
chip antibody: 4H8 (Abcam, catalog# ab5408)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and RNAP2-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample preparation kit (Part# PE-940-2005).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequencing reads were trimmed down to 36bp and then mapped against the male set of human chromosomes (excluding all random chromosomes and haplotypes) using the hg19 version of the human genome as a reference
Bowtie 0.12.7 was used for aligning reads, with the following settings: "-v 2 -t --best --strata".
ChIP-seq peaks were called using MACS2 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files: Signal profiles over genomic locations were generated using custom written python scripts; the refSeq annotation was used for gene coordinates.
|
| |
|
| Submission date |
Jan 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Fei Yang |
| Organization name |
California Institute of Technology
|
| Street address |
1200 E. California Blvd.
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE43253 |
Antitumor activity of a pyrrole-imidazole polyamide |
|
| Relations |
| SRA |
SRX213869 |
| BioSample |
SAMN01881944 |
| Named Annotation |
GSM1059396_LNCaP_Nontreated_br2.bigWig |
