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Series GSE143026 Query DataSets for GSE143026
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
Submission date Jan 03, 2020
Last update date Mar 16, 2022
Contact name Michael M. Hoffman
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)
GSM4249068 CTCF ChIP-seq_93-VU147T_R1
GSM4249069 CTCF ChIP-seq_Caski_R1
GSM4249070 CTCF ChIP-seq_HMS-001_R1
BioProject PRJNA598867
SRA SRP239424

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

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
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Processed data are available on Series record

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