GSE112021   Details

GSE Accession GSE112021
Title Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks (ChIP-Seq)
Submission Date 3/19/18
Last Update Date 3/22/18
Pubmed ID
Experiment Type Genome binding/occupancy profiling by high throughput sequencing
Contributor Elana,J,Fertig; Daria,A,Gaykalova; Joseph,A,Califano; Alexander,V,Favorov
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Contact E-mail
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Organism Homo sapiens
Organism ID 9606
Organism Synonym man; human
Summary Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis.
Overall Design ChIP-sequencing data for 2 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047) for H3K4me3, H3K9ac, H3K9me3, and H3K27ac histone marks; ----------------------------------------------; Submitter declares that the raw data will be submitted to dbGaP ( because of patient privacy concerns.
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