|
| Status |
Public on Feb 20, 2023 |
| Title |
lung_SARS-CoV2pos_2dpi |
| Sample type |
SRA |
| |
|
| Source name |
left lung lobe
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: left lung lobe
virus strain: 2019_nCoV Muc-IMB-1
cell type: tissue homogenizate
time: 2 dpi
Sex: male
|
| Treatment protocol |
21 hamsters were infected orotracheally as described earlier (Blaurock et al., 2022) with 10^5 TCID50 of the ancestral SARS-CoV-2 (isolate 2019_nCoV Muc-IMB-1) per animal. Tissues from infected animals killed at day 1-7 and day 14 as well as mock-infected hamsters killed at day 7 were included in the study (n=3 per day). The left lung lobe was carefully removed, immersion-fixed in 10% neutral-buffered formalin, paraffin-embedded, and 2–3-μm sections were stained with hematoxylin and eosin (HE) for light microscopical examination. In parallel RNA extraction and Illumina RNAseq was performed.
|
| Growth protocol |
Male 5-7 weeks old Syrian gold hamsters (Mesocricetus auratus, raised by Janvier Labs, France) were kept in groups of three to four individuals. Animals were offered water and rodent pellets ad-libitum, fresh hay was offered daily. They were checked for clinical scores, body weight and body temperature on a daily basis. All animals were tested negative for SARS CoV-2 genome in oral and anal swabs and antibodies prior to the experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from homogenized samples using Direct-zol RNA Miniprep Kit (Zymo research, Freiburg, Germany) following manufacturer’s instructions. Extracted RNAs from 3 animals per group were pooled prior to library construction.
Polyadenylated RNAs were isolated with the NEBNext Poly(A) mRNA module (New England Biolabs) and a modified protocol of the NNSR priming method was used to produce cDNA libraries. Sequencing was performed on an Illumina NextSeq550 instrument with a 86 base, single-end setting, using a custom sequencing program.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
All RNAseq analysis steps were performed using CLC Genomics workbench v22.0.2 (Qiagen, Hilden, Germany). Raw fastq reads were checked for quality and trimmed accordingly.
Due to insufficient RNA depletion during library preparation for some samples, trimmed reads were mapped to 28S ribosomal RNA (LOC121137942) to delplete any contaminating rRNAs. Remaining unmapped reads were then mapped to the golden hamster scaffold BCM_Maur_2.0.
Assembly: BCM_Maur_2.0
Supplementary files format and content: csv files with read counts and RPKM values
|
| |
|
| Submission date |
Feb 15, 2023 |
| Last update date |
Feb 21, 2023 |
| Contact name |
Daniel Todt |
| E-mail(s) |
daniel.todt@rub.de
|
| Phone |
+492343222463
|
| Organization name |
Ruhr University Bochum
|
| Department |
Molecular & Medical Virology
|
| Street address |
Universitätsstr. 150
|
| City |
Bochum |
| ZIP/Postal code |
44801 |
| Country |
Germany |
| |
|
| Platform ID |
GPL29592 |
| Series (1) |
| GSE225382 |
Spatiotemporal analysis of SARS-CoV-2 infection in hamster lungs reveals an expansive wave of monocyte-derived macrophages associated with vascular damage and virus clearance |
|
| Relations |
| BioSample |
SAMN33315938 |
| SRA |
SRX19383444 |
