|
| Status |
Public on Feb 05, 2016 |
| Title |
UMSCC1 NTsh |
| Sample type |
SRA |
| |
|
| Source name |
HPV- RNA-Seq Control
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Head and Neck Squamous Cell Carcinoma
dek status: Control
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 |
SAMN03837124 |
| SRA |
SRX1079057 |
