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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2023 |
| Title |
RNA-seq, Early set, 1 dpi, rep 4 |
| Sample type |
SRA |
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| Source name |
Lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Lung
strain: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)
treatment: SARS-CoV-2 infection
time: 1 day post-infection
library type: RNA-seq
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| Treatment protocol |
The mice were lightly anaesthetized with ketamine (20 mg/kg) and xylazine (10 mg/kg) during the infection. All mice were infected intranasally with viruses in a total volume of 50 ìl DMEM. The mice were sacrificed with a CO2 chamber on 0, 1st, 2nd, 5th, and 7th days post-infection (DPI).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Quick-freeze-applied lung tissue samples were homogenized within the lysis buffer (10 mM/mL Tris-HCl pH 7.4 (AM9850G, AM9855G Invitrogen), 5 mM/mL MgCl2 (#AM9530G Ambion), 100 mM/mL KCl (#AM9640G Ambion), 2 mM/mL dithiothreitol (DTT, #707265ML ThermoFisher), 300 μg/mL cycloheximide (CHX, #C1988-1G Sigma-Aldrich), 1% Triton X-100 (#T8787 Sigma-Aldrich), 1X protease inhibitor (#P3100-001 GenDEPOT), 2 μL/mL SUPERase inhibitor (#AM2696, Invitrogen) and 2 μL/mL RNase inhibitor (#AM2694 Invitrogen)) for five minutes on ice followed by incubation at 4°C for 30 minutes with the additional lysis buffer which contained 3 times less amount of CHX. After incubation, samples were spun down and the supernatant was divided into two parts each for RNA-seq and Ribo-seq. The half for RNA-seq was treated with TRIzol LS (#10296028 Invitrogen).
After the purification of RNA from TRIzol-treated samples, libraries were constructed with TruSeq Stranded Total RNA Library Prep Gold (#20020599 Illumina) as per the manufacturer’s protocol, and then sequenced by the NovaSeq 6000 system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
D1d
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| Data processing |
RNA-seq reads that are mapped to the contaminant sequences, including rRNA, tRNA, and srpRNA, using hisat2 were filtered out.
Filtered RNA-seq reads (forward strand only) were mapped to both mouse (GRCm39) and SARS-CoV-2 genome (NC_045512.2) using hisat2.
RNA-seq reads that are mapped within the repeat regions (repeatmasker) were filtered out.
The number of RNA-seq reads mapped to CDS regions of host nuclear genes was counted using featureCounts.
Assembly: Mouse (GRCm39) and SARS-CoV-2 (NC_045512.2)
Supplementary files format and content: Comma-delimited text files include read count values for each sample
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| Submission date |
Jan 05, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Hyeshik Chang |
| E-mail(s) |
hyeshik@snu.ac.kr
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| Organization name |
Seoul National University
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| Department |
School of Biological Sciences
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| Lab |
Hyeshik Chang Lab
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| Street address |
Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| State/province |
South Korea |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE222251 |
Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology (RNA-Seq) |
| GSE222252 |
Heterogeneous ribonucleoprotein interactions and impeded translational elongation in the respiratory tissue of SARS-CoV-2 pathology |
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| Relations |
| BioSample |
SAMN32603045 |
| SRA |
SRX18945607 |
| 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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