|
| Status |
Public on Oct 30, 2018 |
| Title |
2dpi-Old_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Mustela putorius furo |
| Characteristics |
age: 48-50 months
cell type: PBMC
infection status: infected with SFTSV CB1/2014
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from PBMCs of mock PBS control- and SFTSV CB1/2014-infected ferrets using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA quantity was assessed by spectrophotometry using Nanodrop 1000 (Thermo Fisher Scientific).
RNA libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina). About 50 millions of paired-end reads with 100-nucleotide length were generated for each sample and sequenced on Illumina Hi-Seq 2500 system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TN1801R7067--CCGTCCCG
|
| Data processing |
Raw sequencing files were filtered for short or poor quality reads, then aligned to the ferret genome using CLC Genomics Workbench Tool (v 11)
Differentially expressed genes were identified using CLC Genomics Workbench Tool. Two-tailed Wald Test was used to calculate the p value. Genes showing altered expression with p < 0.05 and more than 2 fold changes were considered differentially expressed.
The pathway and network analysis was performed using Ingenuity (IPA). IPA computes a score for each network according to the fit of the set of supplied focus genes.Â
The canonical pathways generated by IPA are the most significant for the uploaded data set.
Genome_build: Ferret genome from Ensembl (MusPutFur1.0)
Supplementary_files_format_and_content: Read counts and differential gene expression in .xlsx format
|
| |
|
| Submission date |
Oct 29, 2018 |
| Last update date |
Oct 30, 2018 |
| Contact name |
Angela Park |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Southern California
|
| Department |
Molecular Microbiology and Immunology
|
| Street address |
1501 San Pablo St, ZNI 521
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL25735 |
| Series (1) |
| GSE121911 |
Ferret animal model of severe fever with thrombocytopenia syndrome phlebovirus for human lethal infection and pathogenesis |
|
| Relations |
| BioSample |
SAMN10340892 |
| SRA |
SRX4948654 |
