|
| Status |
Public on Nov 16, 2021 |
| Title |
infected with TIP pre-treat rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
lung tissue
|
| Organism |
Mesocricetus auratus |
| Characteristics |
agent: infected with SARS-CoV-2
treatment: LNPs containing TIP RNA
|
| Treatment protocol |
Samples 1-10: 8-week old syrian golden hamsters were infected through intranasal installation of 10^6 total PFU per animal of SARS-CoV-2 (USA-WA1/2020) 100 ml of DMEM, as described (Rogers et al., 2020). 6 hours pre-infection and 18 hours post infection animals were given an intranasal dose of 100 ml of LNP solution containing 60 mg of either TIP RNA (hamsters n=5; samples 1-5) or control RNA (hamsters n=5; samples 6-10). For uninfected samples; 8-week old syrian golden hamsters were intranasally treated with TIP (hamsters n=3; samples 11-13) or control RNA LNPs (hamsters n=3; samples 14-16). At day-5 post-infection, animals were sacrificed and lungs were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were homogenized, RNA was extracted from the lung lysates using Direct-zol RNA extraction kit.
RNA libraries were prepared using Illumina Stranded total RNA library prep kit (cat# 20040525, Illumina inc.) and sequencing performed on a NextSeq 500 sequencer (cat# SY-415-1001, Illumina Inc).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Inf_T3
|
| Data processing |
Read quality was checked via FASTQC, followed by mapping to MesAur1.0 (GCA_000349665.1) reference genome using STAR (STAR-2.7.9a) with default parameters.
Transcript level quantification was performed using featureCounts (subread-2.0.2) with default parameters.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Text files for raw gene counts for each individual samples.
Supplementary_files_format_and_content: Excel file for a matrix table containing normalized gene counts across all samples.
|
| |
|
| Submission date |
Sep 20, 2021 |
| Last update date |
Nov 16, 2021 |
| Contact name |
Xinyue Chen |
| Organization name |
Gladstone Institutes
|
| Street address |
1650 Owens St
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL24490 |
| Series (1) |
| GSE184447 |
Analysis of the antiviral activity of TIP against SARS-CoV2 in Mesocricetus auratus |
|
| Relations |
| BioSample |
SAMN21521772 |
| SRA |
SRX12260719 |
