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Series GSE112023 Query DataSets for GSE112023
Status Public on Mar 20, 2018
Title A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers (MBD-Seq)
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary The incidence of HPV-related oropharyngeal squamous cell carcinoma (OPSCC) has increased more than 200% in the past 20 years. Recent genetic sequencing efforts have elucidated relevant genes in head and neck cancer, but HPV-related tumors have consistently shown few DNA mutations. In this study, we sought to analyze alternative splicing events (ASE) that could alter gene function independent of mutations. To identify ASE unique to HPV-related tumors, RNA sequencing was performed on 46 HPV-positive OPSCC and 25 normal tissue samples. A novel algorithm using outlier statistics on RNA-sequencing junction expression identified 109 splicing events, which were confirmed in a validation set from The Cancer Genome Atlas.
 
Overall design MBD-sequencing data for 50 HPV+ HNSCC tumors, 25 normal UPPP, 2 HPV+ HNSCC patient derived xenografts, and 2 HPV+ HNSCC cell lines (SCC-090, SCC-047)
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Submitter declares that the raw data from patients will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.
 
Contributor(s) Fertig EJ, Gaykalova DA, Califano JA, Favorov AV
Citation(s) 31097695
Submission date Mar 19, 2018
Last update date May 29, 2019
Contact name Elana Judith Fertig
E-mail(s) ejfertig@jhmi.edu
Organization name Johns Hopkins University
Department Oncology Quantitative Sciences
Street address 550 N Broadway, Suite 1101E
City Baltimore
State/province MD
ZIP/Postal code 21209
Country USA
 
Platforms (1)
GPL20148 AB 5500xl-W Genetic Analysis System (Homo sapiens)
Samples (79)
GSM3052995 HPV+ HNSCC tumor MBD-Seq sample 1
GSM3052996 HPV+ HNSCC tumor MBD-Seq sample 2
GSM3052997 HPV+ HNSCC tumor MBD-Seq sample 3
This SubSeries is part of SuperSeries:
GSE112027 HPV
Relations
BioProject PRJNA438962
SRA SRP136011

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE112023_RAW.tar 124.0 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA

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