|
Status |
Public on May 05, 2014 |
Title |
NOD_PR8_D4_30 |
Sample type |
SRA |
|
|
Source name |
lung
|
Organism |
Mus musculus |
Characteristics |
strain: NOD virus: PR8 day-post-infection: D4
|
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 |
SAMN02402919 |
SRA |
SRX377839 |