|
| Status |
Public on Jun 28, 2024 |
| Title |
F d30 5 [F30-5] |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: skeletal muscle
infection: H1N1 influenza A virus (A/California/04/2009, IAV)
timepoint: d30
|
| Treatment protocol |
When the hamsters reached 10 weeks of age, they were divided into three cohorts: 1) mock treatment group: intranasally infected with PBS; 2) SARS-CoV-2-infected group: intranasally infected with 1000 pfu (total volume 100 μL) of SARS-CoV-2 (USA-WA1/2020); and 3) IAV-infected group: intranasally infected with 100,000 pfu (total volume 100 μL) of H1N1 IAV (A/California/04/2009). Intranasal administration was performed under ketamine/xylazine anesthesia. Hamsters were housed for 3, 30, and 60 days post-infection before being euthanized via sodium pentobarbital and intracardiac perfusion with PBS (with severed inferior vena cava).
|
| Growth protocol |
Six to eight week-old male Golden Syrian hamsters (Mesocricetus auratus) were obtained from Charles River Laboratories. Hamsters were acclimated to the CDC/USDA-approved Biosafety Level 3 (BSL-3) facility at the Center for Comparative Medicine and Surgery (CCMS) at Icahn School of Medicine at Mount Sinai (New York, NY, USA) for at least 14 days.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
After perfusion, quadriceps muscle (ventral thigh) was exposed and harvested. Samples for RNA extraction were placed into "lysing matrix A" homogenization tubes (MP Biomedicals) filled with TRIzol and homogenized before being frozen at -80oC. RNA was later isolated from homogenized muscle samples by TRIzol/phenol-chloroform extraction.
100 nanograms of total RNA from each sample was enriched for polyadenylated RNA and prepared for next-generation sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
STAR (version 2.7.9a) was used to align sequence reads to golden hamster genome build MesAur1.0 (NCBI accession GCF_000349665.1).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 105 (uniquely aligned proper pairs, same strand).
Variance-stabilizing-transformed (VST) expression values were computed using the DESeq2 R package (version 1.32.0).
Assembly: MesAur1.0
Supplementary files format and content: counts.txt: 22246 x 21 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 22246 x 21 matrix of variance-stabilizing-transformed (VST) expression values
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL33389 |
| Series (1) |
| GSE231910 |
Respiratory SARS-CoV-2 Infection Induces Skeletal Muscle Atrophy and Long-Lasting Energy Metabolism Suppression |
|
| Relations |
| BioSample |
SAMN34996178 |
| SRA |
SRX20251604 |
