GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM6918989 Query DataSets for GSM6918989
Status Public on Dec 01, 2023
Title RNA-seq, Late set, control, rep 2
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: None
time: None
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 Ctl2b
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
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
BioSample SAMN32603039
SRA SRX18945613

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap