|
| Status |
Public on Apr 10, 2020 |
| Title |
Series14_FerretTrachea_IAV_d3_6 |
| Sample type |
SRA |
| |
|
| Source name |
IAV infected 4 month old Ferret
|
| Organism |
Mustela putorius furo |
| Characteristics |
tissue/cell type: Trachea
treatment: IAV infected (1E5 PFU)
strain: A/Texas/71/2017, clade 3C.3a (H3N2)
time after treatment: 3 days
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TruSeq Stranded mRNA LP
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mf-trachea-H3N2-3d-F533-2
processed data file: RawReadCounts_Ferret.tsv
|
| Data processing |
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.
|
| |
|
| Submission date |
Apr 08, 2020 |
| Last update date |
Apr 12, 2020 |
| Contact name |
Daniel Blanco Melo |
| Organization name |
Icahn School of Medicine at Mount Sina
|
| Department |
Microbiology
|
| Lab |
tenOever Lab
|
| Street address |
One Gustave L. Levy Place, Box 1124
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL28369 |
| Series (1) |
| GSE147507 |
Transcriptional response to SARS-CoV-2 infection |
|
| Relations |
| BioSample |
SAMN14563391 |
| SRA |
SRX8089340 |
