|
| Status |
Public on Jun 22, 2016 |
| Title |
HepG2 treated detection of p53 binding sites |
| Sample type |
SRA |
| |
|
| Source name |
Human liver carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
transduction: HBV HBx protein expressing
antibody: p53 FL-393 antibody
antibody vendor: Santa Cruz Biotechnology
antibody catalog number: sc-6243
|
| Treatment protocol |
The cells were transduced with HBx-expressing or control adenovirus, treated with UVC (254nm) irradiation 48 h post-transduction and harvested 24 h after UV irradiation
|
| Growth protocol |
HepG2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% foetal calf serum.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with p53 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Alignment to human genome through BWA
SAM to BAM conversion using samtools
Peak-calling using MACS (version 2.0.9)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: peaks.bed
|
| |
|
| Submission date |
Jan 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Thurnherr |
| E-mail(s) |
thomas.thurnherr@gmail.com
|
| Organization name |
NCCS
|
| Lab |
LCFG
|
| Street address |
11 Hospital Drive
|
| City |
Singapore |
| ZIP/Postal code |
169610 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE64877 |
Global re-wiring of p53 transcription regulation by the hepatitis B virus X (HBx) protein [ChIP-Seq] |
| GSE64878 |
Global re-wiring of p53 transcription regulation by the hepatitis B virus X (HBx) protein |
|
| Relations |
| BioSample |
SAMN03281300 |
| SRA |
SRX838192 |
