|
| Status |
Public on Mar 06, 2024 |
| Title |
Superinfection (Superinfected_5.125_2) |
| Sample type |
SRA |
| |
|
| Source name |
C57BL/6J
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Lungs
time (days after first infection): 5.125
infection: Superinfection
|
| Treatment protocol |
Mice were anesthetized intraperitoneally with ketamine and xylazine cocktail and subjected to four treatments: PBS control, IAV alone, S. pneumoniae alone, and IAV infection followed by S.pneumoniae infection.
|
| Growth protocol |
Virus was grown in allantoic fluid of 10-day-old embryonated chicken eggs at 37°C for 72 h. Allantoic fluid was harvested and viral titres were determined by standard plaque assay in Madin–Darby canine kidney. S. pneumoniae (ATCC 6303, a type 3 encapsulated strain) was grown for 16 h at 370C in 5% CO2 on Columbia Agar plates supplemented with 5% (vol/vol) sheep blood.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung tissues were collected into RNAlater (Qiagen). Lysis was performed with QIAzol (Qiagen). RNA isolation was performed according to miRNeasy kit protocol (Qiagen).
mRNA quality was checked using the Agilent 2100 Bioanalyzer according to the manufacturer’s instructions. All RNA Integrity Numbers (RINs) were higher than 8. cDNA libraries were prepared using 2µg of isolated RNA according to the manufacturer’s instructions of the SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen). DNA size and quality were checked using the Agilent 2100 Bioanalyzer, according to the manufacturer’s instructions. Libraries were quantified by using the Qubit DNA HS Assay kit (Invitrogen). The amplified libraries, each sample having its own index primer, were pooled at a total concentration of 2 nM and sequenced using the Illumina HiSeq platform (Technion Genome Center, Israel).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
We applied a joint alignment of sequencing reads for both the mouse genome and the influenza virus genome, and then applied a joint quantification of both the virus and mouse transcripts.
Raw counts were derived with featureCounts. Raw read counts were imported into R studio and were then normalized using DESeq2 package
Assembly: mm9
Supplementary files format and content: comma-delimited csv file including DESeq2 normalized reads
|
| |
|
| Submission date |
Jun 21, 2022 |
| Last update date |
Mar 06, 2024 |
| Contact name |
ofir cohn |
| E-mail(s) |
[email protected]
|
| Organization name |
Tel Aviv University
|
| Street address |
Tel Aviv University
|
| City |
Tel Aviv |
| ZIP/Postal code |
634121 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE206534 |
Characterization of the host defense against influenza virus infection and a secondary bacterial pneumonia infection |
|
| Relations |
| BioSample |
SAMN29220879 |
| SRA |
SRX15806178 |
