|
Status |
Public on Oct 26, 2016 |
Title |
ChIP-seq Input C42B rep2 |
Sample type |
SRA |
|
|
Source name |
Human prostate cancer cell line C42B
|
Organism |
Homo sapiens |
Characteristics |
cell line: C42B antibody: none
|
Growth protocol |
C42B cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum.
|
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 NextSeq 500 |
|
|
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 |
GPL18573 |
Series (1) |
GSE78913 |
Tracing Enhancer Networks using Epigenetic Traits (TENET) |
|
Relations |
BioSample |
SAMN04532551 |
SRA |
SRX1613578 |