|Public on Feb 05, 2016
|HPV- RNA-Seq Control
|diagnosis: Head and Neck Squamous Cell Carcinoma
dek status: Control
hpv status: HPV-
|At 30% confluency wells were infected with shRNA for NTsh or DEKsh and selected with puromycin. After selection, cells were plated and pellets collected at similar cell numbers for RNA extraction.
|Cells lines are grown in complete DMEM (UMSCC47) or complete DMEM supplemented with 1% hydrocortisone (UMSCC1).
|RNA was extracted with the Zymo RNA mini-prep kit. This included a Dnase digestion. Final RNA was aliquoted and submitted for quality control and RNA-Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|Illumina HiSeq 2500
|Samples were sequenced at the CCHMC DNA core, on an Illumina HiSeq2500 and is based on the TopHat/Cufflinks pipeline. Refence annotation is based on UCSC known genes table.
BAM files from RNA-Seq were imported into GeneSpring NGS software (v12.6) and aligned to hg19/GRCh37 reference genome. Reference annotations produced by Emsembl. Aligned reads were filtered on base quality >=30.
Aligned read couts quantified and used to compute RPKMS. Normalized using DESeq algorithm and threshold set to 1. Filtrations removes all genes with fewer than 3 reads in each sample.
Fold change was calculated as DEKsh/NTsh with a cut-off of 1.4 fold change.
Supplementary_files_format_and_content: TXT files containing UMSCC1 and UMSCC47 normalized values, gene symbols, and Emsembl IDS
|Jul 01, 2015
|Last update date
|May 15, 2019
|Cincinnati Children's Hospital Medical Center
|3333 Burnet Ave.
|Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC)