|
| Status |
Public on May 26, 2022 |
| Title |
Virus3_2 |
| Sample type |
SRA |
| |
|
| Source name |
The lung tissue with SARS-CoV-2 infection (3 days after infection)
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: Lung
treatment: SARS-CoV-2 infection
Sex: male
|
| Treatment protocol |
Infection protocol: Male Syrian golden hamsters aged 7 weeks (190–230 g) were used as a wild-type (WT) animal model. To induce viral infections, WT hamsters were inoculated with SARS-CoV-2 (2.5 x103 TCID50/ml in 30 μl of phosphate-buffered saline [PBS]) by intranasal delivery to induce acute viral lung infections.
The nasal cavities of Syrian golden hamsters (N=3 in each of four groups) were inoculated with recombinant IFN-λ (IFN-λ2: 5 μg, IFN-λ3: 5 μg with 30 μl of PBS) immediately after SARS-CoV-2 infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cell lysate in the lungs of SARS-CoV-2-infected hamsters at indicated timepoints using TRIzol. cDNA was synthesized from 1 μg of RNA with random hexamer primers using Moloney murine leukemia virus reverse transcriptase.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Mesocricetus auratus whole genome using Tophat
Read count extraction and Quantile nomalization were performed using edgeR.
Assembly: Mesocricetus auratus
Supplementary files format and content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
May 24, 2022 |
| Last update date |
May 27, 2022 |
| Contact name |
Hyun Jik Kim |
| E-mail(s) |
hyunjerry@snu.ac.kr
|
| Phone |
+82-2-2072-2203
|
| Organization name |
Seoul National University
|
| Department |
Department of otorhinolaryngology
|
| Street address |
101 Daehak-ro, Jongno-gu
|
| City |
Seoul |
| ZIP/Postal code |
110-744 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24490 |
| Series (1) |
| GSE204696 |
Bulk RNA sequencing in SARS-CoV-2-infected hamsters |
|
| Relations |
| BioSample |
SAMN28635255 |
| SRA |
SRX15437220 |
