|
| Status |
Public on Apr 06, 2022 |
| Title |
FMB_3005_D2 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Mustela putorius furo |
| Characteristics |
Sex: Male
age: Adult
ferretid: 3005
day: -2
infectionagent: A/California/07/2009
viralload: 0
relweight: NA
tissue: whole blood
|
| Treatment protocol |
Adult ferrets were infected intranasally with the A/California/07/2009 virus at a dose of 106 plaque-forming units (PFU). The animals were monitored daily for the severity of clinical disease using weight loss.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from ferret blood using the Mouse RiboPure-Blood RNA Isolation Kit (Ambion)
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer-supplied protocol. Libraries were sequenced 100 bp paired-end to a depth of approximately 40 million host genome reads on Illumina HiSeq 2500 instruments.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired-end reads were aligned to ferret genome Ensembl version 1.0.80 using tophat (version v2.0.13)
Following read alignment, featureCounts (v1.4.6) was used to quantify the mRNA expression levels based on Ensembl gene model.
mRNAs with more than 5 reads in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: ferret genome Ensembl version 1.0.80
Supplementary_files_format_and_content: normalized.log2CPM.tsv (tab-delimited file using log2-transformed CPM values for each sample)
|
| |
|
| Submission date |
Mar 02, 2021 |
| Last update date |
Apr 06, 2022 |
| Contact name |
Christian Forst |
| E-mail(s) |
christian.forst@mssm.edu
|
| Phone |
212-824-8948
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Street address |
One Gustave L. Levy Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL25735 |
| Series (2) |
| GSE168117 |
Sex disparities in influenza: a multiscale network analysis (Male ferrets) |
| GSE168512 |
Sex disparities in influenza: a multiscale network analysis |
|
| Relations |
| BioSample |
SAMN18115023 |
| SRA |
SRX10213854 |
