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| Status |
Public on May 27, 2014 |
| Title |
IM012_10_PBS_3_WT |
| Sample type |
SRA |
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| Source name |
lung, PBS, 12 hr
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J
age: 6 weeks
tissue: lung
treatment: PBS
time post treatment: 12 hr
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| Treatment protocol |
Intranasally dosed (10,000 U of recombinant interferon) or mock dosed (PBS).
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| Growth protocol |
Whole animal.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy Isolation Kit from Trizol homogenates.
Illumina TruSeq mRNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
total RNA
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| 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.
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| Submission date |
Feb 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Katze |
| E-mail(s) |
data@viromics.washington.edu
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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 |
GPL11002 |
| Series (1) |
| GSE55480 |
RNA-seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis |
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| Relations |
| BioSample |
SAMN02666865 |
| SRA |
SRX478892 |
| 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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