|
| Status |
Public on Oct 26, 2016 |
| Title |
ChIP-seq Input RWPE1 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human prostate cell line RWPE1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RWPE1
antibody: none
|
| Growth protocol |
RWPE1 cells were grown in medium following ATCC recommended conditions: Keratinocyte Serum Free Medium (K-SFM), Kit Catalog Number 17005-042 (GIBCO) which supplies bovine pituitary extract (BPE) and human recombinant epidermal growth factor (EGF).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, cells were crosslinked using 1% formaldehyde and lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were barcoded (NEXTflex™ DNA Barcodes) (Bio Scientific, Austin, TX).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq reads were aligned to hg19 genome assembly using bwa.
For ChIP-seq, Sole-Search (alpha=0.0001, FDR=0.0001, peakmergedistance=0, histoneblurlength=1200) was used to call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, tab-delimited text files include location of peaks
|
| |
|
| Submission date |
Mar 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Suhn K Rhie |
| Organization name |
University of Southern California
|
| Street address |
1450 Biggy Street
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE78913 |
Tracing Enhancer Networks using Epigenetic Traits (TENET) |
|
| Relations |
| BioSample |
SAMN04532557 |
| SRA |
SRX1613584 |
