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| Status |
Public on Mar 30, 2021 |
| Title |
TPT_INFECTED_D6_rep3 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mesocricetus auratus |
| Characteristics |
infection: Infected
treatment: TPT
time point: Day 6
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| Treatment protocol |
Female Golden Syrian hamster, aged 6-8 week old (~70-100g), were obtained from Laboratory Animal Unit, University of Hong Kong (HKU). All experiments were performed in a Biosafety Level-3 animal facility, LKS Facility of Medicine, HKU. The study has been approved by the Committee on the Use of Live Animals in Teaching and Research, HKU. Virus stock was diluted with Phosphate-buffered saline (PBS) to 2 x 104 PFU/ml. Hamsters were anesthetized with ketamine (150mg/kg) and xylazine (10 mg/mg) and then intranasally inoculation with 50 ul of diluted viruses containing 103 PFU of viruses. For drug treatments, 10mg/kg TPT resuspended in vehicle [5% DMSO + 5% corn oil in PBS] or vehicle alone was administered intraperitoneally to animals on the indicated days post infection.
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| Growth protocol |
NA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Infected hamsters that were treated with TPT or vehicle control were euthanized at days 4 and 6 post infection. Uninfected hamsters were used as controls. After euthanasia, lung left inferior lobe from hamsters were cut into pieces and lysed with RA1 lysis buffer provided with the NucleoSpin® RNA Plus kit (Macherey-nagel), RNA extraction was performed according the manufacturer’s recommendations, including an on-column genomic DNA digestion step.
RNA sequencing library preparation and sequencing were then performed by BGI Genomics
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
V300055997_LC_HK500MOUccoEAARRAAPEI-518
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| Data processing |
After adaptor removal with cutadapt (Martin, 2011) and base-quality trimming to remove 3′read sequences if more than 20 bases with Q <20 were present, paired-end reads were mapped to the SARS-CoV-2 and hamster (MesAur1.0, reference genomes with STAR . Gene-count summaries were generated with featureCounts (Liao et al., 2014). A numeric matrix of raw read counts was generated, with genes in rows and samples in columns, and used for differential gene expression analysis with the Bioconductor Limma package.
Genome_build: MesAur1.0 ; Sars_cov_2.ASM985889v3
Supplementary_files_format_and_content: tab delimited table of raw counts for each sample
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| Submission date |
Dec 03, 2020 |
| Last update date |
Mar 30, 2021 |
| Contact name |
Sook Yuin Jessica Ho |
| E-mail(s) |
sook.ho@mssm.edu
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Department |
Microbiology
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| Lab |
Ivan Marazzi
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| Street address |
1468 Madison Avenue
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10028 |
| Country |
USA |
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| Platform ID |
GPL24490 |
| Series (2) |
| GSE162618 |
Role of Top1 and Genome structure in SARS-CoV-2 infection [RNA-Seq hamster] |
| GSE162619 |
Role of Top1 and Genome structure in SARS-CoV-2 infection |
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| Relations |
| BioSample |
SAMN16988751 |
| SRA |
SRX9627379 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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