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Status |
Public on Sep 05, 2023 |
Title |
SRK017-10 |
Sample type |
SRA |
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Source name |
gastrocnemius muscle
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Organism |
Mus musculus |
Characteristics |
tissue: gastrocnemius muscle age: Aged days post_infection: 0 treatment: infected with 500 EID50 of PR8 infuenza
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Treatment protocol |
Young (n=10/time point) and aged (n=9–10/time point) C57BL/6 mice were intranasally infected with 500 EID50 of PR8 infuenza and analyzed at various DPI. The gastrocnemius muscle was harvested at various days post infection (DPI) and RNA was isolated
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Extracted molecule |
total RNA |
Extraction protocol |
The gastrocnemius muscle was dissected and placed in RNAlater (Qiagen Inc., Germantown, MD) overnight at 4 °C. RNAlater was removed the following day, and the muscle was frozen at−80°C until RNA isolation. The muscle was homogenized and RNA was extracted via miRNeasy extraction per manufacturer’s instructions (Qiagen Inc., Germantown, MD). mRNA-seq libraries were structured according to the standard Illumina TruSeq-stranded mRNA protocol from 2 rounds of the same experiment run together
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Description |
SRK017-10.counts
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Data processing |
Paired-end 151-bp sequencing was performed on an Illumina HiSeq 2000 (Illumina, Shelton, CT). Sequencing reads were trimmed with trimmomatic (Bolger, Lohse et al. 2014) to remove the universal Illumina adaptor and mapped to the UCSC mouse reference genome (mm9) and a custom splice junction library in parallel using hisat2/2.1.0 We continued our analysis with samples that contained at least 36 million mapped reads. Uniquely Mapped reads were quantifed using HTSeq Genes were considered not expressed if they had zero reads in all technical and biological replicates. Mapped reads in were counted using HTSeq and then diferential expression was performed with DESeq2 Assembly: mm9 Supplementary files format and content: comma separated values (.csv) file includes raw counts for each sample
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Submission date |
Aug 30, 2023 |
Last update date |
Sep 05, 2023 |
Contact name |
Laura Haynes |
E-mail(s) |
lhaynes@uchc.edu
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Organization name |
UCONN Health
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Department |
Center on Aging
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Street address |
263 Farmington Avenue
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City |
Farmington |
State/province |
CT |
ZIP/Postal code |
06030 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE241965 |
Altered T cell infiltration and enrichment of leukocyte regulating pathways within aged skeletal muscle are associated impaired muscle function following influenza infection |
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Relations |
BioSample |
SAMN37202845 |
SRA |
SRX21539508 |
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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