|
| Status |
Public on Mar 29, 2023 |
| Title |
Infected, 37°C, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
olfactory nerve-derived cell
|
| Organism |
Myotis myotis |
| Characteristics |
cell type: olfactory nerve-derived cell
temperature: 37
infection: EBLV-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After a total of 54h post-infection (hpi), the supernatants were collected and stored at −80◦C. The cells were lysed with 1 mL of TRIzol (ThermoFisher) and RNA was extracted using Direct-zol RNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions (including a DNAse I treatment), and eluted into 50 µL RNAse free water.
Strand-specific single-end cDNA libraries were prepared using TruSeq Stranded mRNA sample prep kit, Illumina according to the manufacturers’ instructions and sequenced using Illumina NextSeq 500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
I37_3
|
| Data processing |
The bioinformatic analysis was performed using the RNA-seq pipeline from Sequana.
Sequencing reads were cleaned of adapter and low-quality sequences using cutadapt version 2.6.
STAR version 2.7.3a was used for the alignment onto the reference genome (Myotis lucifugus 2.0 on Ensembl 99)
featureCounts version 2.0.0 was used to count the number of reads mapped on each gene.
Count data were analyzed using R version 3.6.1 and the Bioconductor package DESeq2 version 1.26.0.
Assembly: Myotis lucifugus 2.0 on Ensembl 99
Supplementary files format and content: Raw counts from featureCounts
|
| |
|
| Submission date |
Mar 28, 2023 |
| Last update date |
Mar 29, 2023 |
| Contact name |
Hugo Varet |
| Organization name |
Institut Pasteur
|
| Street address |
28 rue du Docteur Roux
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL33286 |
| Series (1) |
| GSE228404 |
Transcriptomic responses of bat cells to European bat lyssavirus 1 infection under conditions simulating euthermia and hibernation |
|
| Relations |
| BioSample |
SAMN33950592 |
| SRA |
SRX19794965 |
