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| Status |
Public on Jun 24, 2024 |
| Title |
Ctrl, DENV1, bodies, day 5, replicate B |
| Sample type |
SRA |
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| Source name |
bodies
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| Organism |
Aedes aegypti |
| Characteristics |
tissue: bodies
genotype: Ctrl
days post_infection: D5
infection: DENV1
replicate: B
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracts from pools of 10 tissues were isolated with TRIzol (Invitrogen) and treated with DNA-free kit (Invitrogen, AM1906) following the manufacturer’s instructions. The quality of the samples was assessed using a BioAnalyzer RNA Nano kit (Agilent Technologies).
RNA libraries were built using an Illumina Stranded mRNA library Preparation Kit following the manufacturer’s protocol depending on the insert size required. All the samples were eluted for 2 minutes at 80°C after polyA capture to obtain 300-bp inserts.
Sequencing was performed on two lanes 10B300 of NovaSeqX (Illumina) by Novogen.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
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| Description |
bodies-day5-DENV1_VLG-1_vs_Ctrl.xlsx
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| Data processing |
Raw RNA-sequencing reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.10 with options "-m 25 -q 30 -O 6 --trim-n --max-n 1".
Gene expression quantification was performed using salmon version 1.9.0. First, the Aedes aegypti reference transcriptome (downloaded from VectorBase 66) was indexed along with its corresponding genome using the "--decoys" option.
Transcript expression was then quantified for each sample using the "-l A" option and summarized at the gene level using the "--geneMap" parameter.
Gene expression data was imported into R version 4.3.2 using the tximport package. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm.
A generalized linear model was set in order to test for the infection effect on the gene expression, separately for WT and Vago mosquitoes. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure.
Assembly: AaegyptiLVP_AGWG from VectorBase 66 (https://vectorbase.org/common/downloads/release-66/AaegyptiLVP_AGWG/fasta/data/)
Supplementary files format and content: Text file containing gene-level expression generated by the salmon software.
Supplementary files format and content: Excel file containing the results of the differential analysis performed with DESeq2 (VLG-1 vs Ctrl).
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| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Hugo Varet |
| Organization name |
Institut Pasteur
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| Street address |
28 rue du Docteur Roux
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| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL34603 |
| Series (1) |
| GSE269945 |
A Vago-like gene enhances dengue and Zika virus dissemination in Aedes aegypti |
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| Relations |
| BioSample |
SAMN41843997 |
| SRA |
SRX24933472 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8330773_59_B_Sis_dv_quant.genes.sf.gz |
264.9 Kb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
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