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Sample GSM2178351 Query DataSets for GSM2178351
Status Public on Feb 13, 2018
Title FLU.H.2014.01.54FUR0056.0d.RNA.Access_S18
Sample type SRA
 
Source name Nasal Swab
Organism Homo sapiens
Characteristics tissue: nasal epithelial cells
infection: H3N2
Extracted molecule total RNA
Extraction protocol Nasal swabs were collected from individuals (n=3) confirmed to be infected with H3N2 viruses. Swabs were taken on the day of diagnosis (d0) as well as 3 and 7 days post-diagnosis.Total RNA was extracted from nasal swabs suspended in RLT buffer using the Qiagen miRNeasy Micro Kit (Qiagen, Valencia, CA).
Libraries for RNA sequencing were constructed using TruSeq RNA Access kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing General quality control of the raw reads was performed using FastQC.
Ribosomal RNA reads were removed via mapping by Bowtie (v2.1.0) (Langmead and Salzberg, 2012) using an index of human, mouse, and rat rRNA sequences
For each sample about 90% of remaining reads were mapped against the human reference genome (hg19, build GRCh37, from the UCSC genome browser using STAR (v2.4.0h1) (Dobin et al., 2013).
Quantitative gene counts were produced utilizing the human annotation associated with the genome using the python package HT-Seq (Anders, Pyl, and Huber, 2015).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of gene abundance
 
Submission date May 26, 2016
Last update date May 15, 2019
Contact name Michael Katze
E-mail(s) data@viromics.washington.edu
Organization name University of Washington
Department Microbiology
Lab Michael G. Katze, Ph.D
Street address Rosen Building 960 Republican St.
City Seattle
State/province WA
ZIP/Postal code 98109-4325
Country USA
 
Platform ID GPL18573
Series (2)
GSE81951 Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells [RNA-Seq]
GSE83285 Evaluation of the immunogenicity of live-attenuated influenza vaccines in nasal epithelial cells in primary differentiated human nasal epithelial cells
Relations
BioSample SAMN05179851
SRA SRX1801740

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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