|
| Status |
Public on Feb 14, 2020 |
| Title |
Viral integration transforms chromatin to drive oncogenesis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We report that the integration of the human papillomavirus into the host genome increases chromatin accessibility, transcription, and CTCF binding within 100 kbp of the integration site which promotes oncogenesis in some patients.
|
| |
|
| Overall design |
We used 5 patient-derived HPV16-positive cell lines. Three biological replicates for CTCF ChIP-seq, 1 lane of sequencing for ATAC-seq of each sample, and 4 lanes of sequencing for RNA-seq of each sample.
|
| |
|
| Contributor(s) |
Karimzadeh M, Arlidge C, Rostami A, Lupien M, Bratman SV, Hoffman MM |
| Citation |
https://doi.org/10.1101/2020.02.12.942755
|
| |
| Submission date |
Jan 03, 2020 |
| Last update date |
Mar 16, 2022 |
| Contact name |
Michael M. Hoffman |
| E-mail(s) |
michael.hoffman@utoronto.ca
|
| Organization name |
University Health Network
|
| Department |
Princess Margaret Cancer Centre
|
| Lab |
Hoffman Lab
|
| Street address |
101 College St PMCRT 11-311
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 1L7 |
| Country |
Canada |
| |
|
| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (30)
|
|
| Relations |
| BioProject |
PRJNA598867 |
| SRA |
SRP239424 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE143026_93-VU147T_ATAC_PEAKS.narrowPeak.gz |
2.5 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_93-VU147T_CTCF_PEAKS.narrowPeak.gz |
789.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_Caski_ATAC_PEAKS.narrowPeak.gz |
2.7 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_Caski_CTCF_PEAKS.narrowPeak.gz |
505.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_HMS001_ATAC_PEAKS.narrowPeak.gz |
3.6 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_HMS001_CTCF_PEAKS.narrowPeak.gz |
829.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_SCC-090_ATAC_PEAKS.narrowPeak.gz |
3.8 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_SCC-090_CTCF_PEAKS.narrowPeak.gz |
599.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_SiHa_ATAC_PEAKS.narrowPeak.gz |
2.7 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_SiHa_CTCF_PEAKS.narrowPeak.gz |
913.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE143026_TPM_MergedRnaSeqMatrix_filtered.tsv.gz |
659.4 Kb |
(ftp)(http) |
TSV |
| GSE143026_metadata.tsv.gz |
2.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...