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Sample GSM1755405 Query DataSets for GSM1755405
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
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)
BioSample SAMN03837125
SRA SRX1079058

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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