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Sample GSM7746727 Query DataSets for GSM7746727
Status Public on Sep 05, 2023
Title SRK017-10
Sample type SRA
 
Source name gastrocnemius muscle
Organism Mus musculus
Characteristics tissue: gastrocnemius muscle
age: Aged
days post_infection: 0
treatment: infected with 500 EID50 of PR8 infuenza
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
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description SRK017-10.counts
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
 
Submission date Aug 30, 2023
Last update date Sep 05, 2023
Contact name Laura Haynes
E-mail(s) lhaynes@uchc.edu
Organization name UCONN Health
Department Center on Aging
Street address 263 Farmington Avenue
City Farmington
State/province CT
ZIP/Postal code 06030
Country USA
 
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
Relations
BioSample SAMN37202845
SRA SRX21539508

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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