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Sample GSM3473067 Query DataSets for GSM3473067
Status Public on Nov 15, 2018
Title SCC15
Sample type SRA
 
Source name HNSCC_HPV_neg
Organism Homo sapiens
Characteristics cell line: SCC15
cell type: head and neck squamous cell carcinoma (HNSCC) cell line
hpv.status: HPV_neg
Extracted molecule total RNA
Extraction protocol RNeasy Plus (Qiagen)
TruSeq Stranded Total RNA Sample Prep Kit (Illumina); 75-bp paired-end (Illumina HiSeq3000)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Alignment was performed using tophat2
Aligment quality was accessed by fastqc, samtools and htseq-qa
Counting reads was using htseq-count with parameters: python -m HTSeq.scripts.count -s no -t exon sortByName.sam.mod REFFILE > OUTFILE
The normalization of raw read counts was performed by edgeR package in R. The procedure was described in limma package in R. The features were first filtered out if the total counts less than 50
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample.
 
Submission date Nov 14, 2018
Last update date Nov 15, 2018
Contact name Curtis Pickering
E-mail(s) crpickering@mdanderson.org
Organization name The University of Texas MD Anderson Cancer Center
Department Head and Neck Surgery
Lab Pickering Lab
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL21290
Series (1)
GSE122512 Gene expression analysis of head and neck squamous cell carcinoma (HNSCC) cell lines.
Relations
BioSample SAMN10422299

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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