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| Status |
Public on Feb 13, 2018 |
| Title |
FLU.H.2014.01.54FUR0065.3d |
| Sample type |
SRA |
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| Source name |
Nasal Swab
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| Organism |
Homo sapiens |
| Characteristics |
tissue: nasal epithelial cells
infection: H3N2
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
May 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Katze |
| E-mail(s) |
[email protected]
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| Organization name |
University of Washington
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| Department |
Microbiology
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| Lab |
Michael G. Katze, Ph.D
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| Street address |
Rosen Building 960 Republican St.
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-4325 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN05179853 |
| SRA |
SRX1801742 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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