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Sample GSM6918994 Query DataSets for GSM6918994
Status Public on Dec 01, 2023
Title RNA-seq, Late set, 5 dpi, rep 3
Sample type SRA
 
Source name Lung
Organism Mus musculus
Characteristics tissue: Lung
strain: B6.Cg-Tg(K18-ACE2)2Prlmn/J (The Jackson Laboratory, #034860)
treatment: SARS-CoV-2 infection
time: 5 days post-infection
library type: RNA-seq
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).
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description D5c
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
 
Submission date Jan 05, 2023
Last update date Dec 01, 2023
Contact name Hyeshik Chang
E-mail(s) hyeshik@snu.ac.kr
Organization name Seoul National University
Department School of Biological Sciences
Lab Hyeshik Chang Lab
Street address Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu
City Seoul
State/province South Korea
ZIP/Postal code 08826
Country South Korea
 
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
Relations
BioSample SAMN32603034
SRA SRX18945618

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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