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Sample GSM1337710 Query DataSets for GSM1337710
Status Public on May 27, 2014
Title IM012_11_IFN_1_mRNA
Sample type SRA
Source name lung, IFN, 12 hr
Organism Mus musculus
Characteristics strain/background: C57BL/6J
age: 6 weeks
tissue: lung
treatment: interferon (IFN)
time post treatment: 12 hr
Treatment protocol Intranasally dosed (10,000 U of recombinant interferon) or mock dosed (PBS).
Growth protocol Whole animal.
Extracted molecule total RNA
Extraction protocol Qiagen miRNeasy Isolation Kit from Trizol homogenates.
Illumina TruSeq mRNA.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Description mRNA
Data processing Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2.
Zipped using gzip.
For mRNA-seq, reads were mapped against the mm9 transcriptome with SOAPaligner/soap2.
For Total RNA-seq, reads were mapped against mm9 using STAR.
HTSeq was used to generate gene counts.
Genome_build: MGSCv37 (mm9), Ensembl release 67.
Supplementary_files_format_and_content: Tab-delimited text file includes: [1] scaled gene counts for each sample of mRNA-seq and [2] scaled gene counts for each sample of Total RNA-seq.
Submission date Feb 28, 2014
Last update date May 15, 2019
Contact name Michael Katze
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)
GSE55480 RNA-seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis
BioSample SAMN02666857
SRA SRX478887

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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