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Sample GSM1937931 Query DataSets for GSM1937931
Status Public on May 13, 2016
Title UM-P13
Sample type SRA
 
Source name squamous cell carcinoma
Organism Homo sapiens
Characteristics tumor stage: IVa
gender: M
hpv-status: HPV16
Extracted molecule total RNA
Extraction protocol Using a sterile scalpel, surface scrapings were taken directly from the frozen tissue blocks from the region of tissue identified as having at least 70% tumor cellularity. Tissue scrapings were processed using the Qiagen AllPrep DNA/RNA/Protein Mini Kit (Valencia, CA, USA) as per manufacturer protocol.
Samples were prepped using the Illumina TruSeq mRNA Sample Prep v2 kit (Catalog #s RS-122-2001, RS-122-2002) (Illumina, San Diego, CA). Where 0.1-3ug of total RNA was converted to mRNA using a polyA purification. The mRNA is then fragmented and copied into first strand cDNA using reverse transcriptase and random primers. The 3 prime ends of the cDNA is then adenylated and adapters are ligated.  One of the adapters that is ligated has a 6 nucleotide barcode that will be unique for each sample which allowed us to sequence more than one sample in each lane of a HiSeq flow cell (Illumina). The products are purified and enriched by PCR to create the final cDNA library. 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA-1.8.2
RNA-Seq reads were aligned to hg19 with tophat2 (v2.0.11) and gene read counts were quantified by HTseq (0.6.1p1) with option “-m intersection-strict” using gene annotation of UCSC hg19.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq read counts were quantified by HTSeq
 
Submission date Nov 12, 2015
Last update date Jul 15, 2021
Contact name Maureen Sartor
E-mail(s) sartorma@umich.edu
Organization name University of Michigan
Street address 100 Washtenaw Ave.
City Ann Abor
ZIP/Postal code 48109
Country USA
 
Platform ID GPL11154
Series (2)
GSE74927 Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures. [RNA-Seq]
GSE74956 Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures.
Relations
BioSample SAMN04261698
SRA SRX1427491

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

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