|
| Status |
Public on Mar 26, 2022 |
| Title |
X53 |
| Sample type |
SRA |
| |
|
| Source name |
Golden hamster 53 (S98)
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: Lung (snap frozen)
virus: None (PBS control)
vaccine: Unvaccinated (PBS control)
volume: 0.5 - 1 mL
dose (vp): Control group
|
| Treatment protocol |
Virus was administered as 100 μl by the intranasal route (50 μl in each nare). Body weights were assessed daily. All immunologic and virologic assays were performed blinded. All animal studies were conducted in compliance with all relevant local, state and federal regulations and were approved by the Bioqual Institutional Animal Care and Use Committee. On day 4, a subset of animals was euthanized for tissue viral loads, pathology and transcriptomics profiling.
|
| Growth protocol |
Seventy male and female Syrian golden hamsters (Envigo), 10–12 weeks old, were randomly allocated to groups. All animals were housed at Bioqual. Animals received Ad26 vectors expressing S.dTM.PP or S.PP or sham controls (n = 10 per group). Animals received a single immunization of 1010 or 109 vp Ad26 vectors by the intramuscular route without adjuvant at week 0. At week 4, all animals were challenged with 5.0 × 105 TCID50 or 5.0 × 104 TCID50 SARS-CoV-2, which was derived with one passage from USA-WA1/2020 (NR-52281, BEI Resources).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung tissue was homogenized in 700 L of QIAzol (Qiagen) and stored at -80°C until being extracted using the miRNeasy Micro kit (Qiagen) with on-column DNase digestion.
RNA quality was assessed using an Agilent Bioanalyzer and ten nanograms of total RNA used as input for library preparation using the SMARTer Stranded Total RNA-Seq V2 Pico Input Mammalian kit (Takara Bio) according to the manufacturer’s instructions. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, targeting 25-30 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Syrian golden hamsters (Envigo), 10–12 weeks old
|
| Data processing |
Alignment was performed using STAR version 2.7.3a with the MesAur1.0 (GCF_000349665.1) assembly and annotation of the hamster downloaded from NCBI. Transcript abundance estimates was calculated internal to the STAR aligner using the algorithm of htseq-count as described previously.
DESeq2 was used for normalization, producing both a raw and normalized read count table. Differential expression at the gene level were performed by DESeq2 implemented in the DESeq2 R package.
A corrected p-value cut-off of 0.05 was used to assess significant genes that were upregulated or down regulated by SARS-CoV-2 at day 4 post challenge in sham and vaccinated animals compared to naïve controls and in vaccinated compared to sham animals using Benjamini-Hochberg (BH) method.
Genome_build: MesAur1.0 (GCF_000349665.1)
Supplementary_files_format_and_content: Raw, and normalized read count tables. File format is .csv.
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Mar 26, 2022 |
| Contact name |
Dan Barouch |
| Organization name |
BIDMC
|
| Department |
CVVR
|
| Lab |
Barouch Lab
|
| Street address |
3 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL28997 |
| Series (1) |
| GSE196893 |
Ad26.COV2.S Prevents SARS-CoV-2 Induced Pathways of Inflammation and Thrombosis in Hamsters |
|
| Relations |
| BioSample |
SAMN25998094 |
| SRA |
SRX14204826 |
