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Status |
Public on May 13, 2016 |
Title |
UM-P13 |
Sample type |
SRA |
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Source name |
squamous cell carcinoma
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Organism |
Homo sapiens |
Characteristics |
tumor stage: IVa gender: M hpv-status: HPV16
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Nov 12, 2015 |
Last update date |
Jul 15, 2021 |
Contact name |
Maureen Sartor |
E-mail(s) |
sartorma@umich.edu
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Organization name |
University of Michigan
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Street address |
100 Washtenaw Ave.
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City |
Ann Abor |
ZIP/Postal code |
48109 |
Country |
USA |
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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. |
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Relations |
BioSample |
SAMN04261698 |
SRA |
SRX1427491 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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