 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 27, 2022 |
| Title |
3 hours post IAV infection, strain 5012A |
| Sample type |
SRA |
| |
|
| Source name |
Lungs
|
| Organisms |
Mus musculus; Influenza A virus (A/Puerto Rico/8/1934(H1N1)) |
| Characteristics |
strain: 5012A
tissue: Lungs
infection: IAV
time: 3 hours post IAV infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Murine lungs were harvested immediately after the time of sacrifice, sliced into small pieces, homogenized using BeadBlaster Microtube Homogenizer (90sec, 4000rpm) in the presence of QIAzol. RNA isolation was then 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 |
| |
|
| Description |
5012A_3
|
| Data processing |
We applied a joint alignment of sequencing reads for both the mouse genome and the influenza virus genome (using the Bowtie2 software), and then applied a joint quantification of both the virus and mouse transcripts. For this quantification, we applied an FPKM-normalization using the RSEM software.
We filtered out duplicate genes by choosing the first appearance of each gene.
Genome_build: mm9, NC_002016, NC_002017, NC_002018, NC_002019, NC_002020, NC_002021, NC_002022, NC_002023
Supplementary_files_format_and_content: comma-delimited csv file including FPKM normalized reads (includes both mouse and IAV genes)
|
| |
|
| Submission date |
May 11, 2021 |
| Last update date |
Dec 27, 2022 |
| Contact name |
Gal Yankovitz |
| E-mail(s) |
galyankovitz@mail.tau.ac.il
|
| Organization name |
Tel-Aviv University
|
| Department |
The Shmunis School of Biomedicine and Cancer Research
|
| Lab |
Gat-Viks
|
| Street address |
Haim Levanon
|
| City |
Tel-Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL30115 |
| Series (1) |
| GSE174253 |
The molecular programs underpinning 'tolerance' and 'resistance' in health and viral infection |
|
| Relations |
| BioSample |
SAMN19107889 |
| SRA |
SRX10856353 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
