|
Status |
Public on Feb 05, 2016 |
Title |
UMSCC1 DEKsh |
Sample type |
SRA |
|
|
Source name |
HPV- RNA-Seq Knockdown
|
Organism |
Homo sapiens |
Characteristics |
diagnosis: Head and Neck Squamous Cell Carcinoma dek status: DEK Knockdown hpv status: HPV-
|
Treatment protocol |
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.
|
Growth protocol |
Cells lines are grown in complete DMEM (UMSCC47) or complete DMEM supplemented with 1% hydrocortisone (UMSCC1).
|
Extracted molecule |
total RNA |
Extraction protocol |
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
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
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. Genome_build: hg19 Supplementary_files_format_and_content: TXT files containing UMSCC1 and UMSCC47 normalized values, gene symbols, and Emsembl IDS
|
|
|
Submission date |
Jul 01, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Susanne Wells |
E-mail(s) |
susanne.wells@cchmc.org
|
Organization name |
Cincinnati Children's Hospital Medical Center
|
Street address |
3333 Burnet Ave.
|
City |
Cincinnati |
State/province |
Ohio |
ZIP/Postal code |
45229 |
Country |
USA |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE70462 |
Identifying DEK-dependent transcriptional signatures in HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC) |
|
Relations |
BioSample |
SAMN03837125 |
SRA |
SRX1079058 |