|
| Status |
Public on May 05, 2014 |
| Title |
PWK_MOCK_D2_115 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: PWK
virus: MOCK
day-post-infection: D2
|
| Treatment protocol |
Intranasally infected or mock infected
|
| Growth protocol |
Whole Animal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy Isolation Kit from Trizol homogenates
Illumina TruSeq Total RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2
Reads were mapped against specific CC founder strain transcriptome with SOAPaligner/soap2 and following command : soap -m 20 -x 500 -r 2 -v 2
To determine fragment count on gene level from SOAP output, we used a custom script in Java reproducing HTSeq paired and strand-specific union mode
Technical replicates were summed
Three samples were excluded based on their low raw gene counts distribution ("PWK_MA15_D2_116", "NOD_MA15_D2_17", "CAST_MA15_D2_99").
Data normalization was performed by scaling as implemented in the DESeq bioconductor package
Genome_build: CC founder pseudogenomes
Supplementary_files_format_and_content: tab-delimited text files include scaled/normalized gene counts for each sample
|
| |
|
| Submission date |
Nov 15, 2013 |
| 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 |
GPL11002 |
| Series (1) |
| GSE52405 |
RNA-Seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis |
|
| Relations |
| BioSample |
SAMN02402931 |
| SRA |
SRX377862 |
