CCS_RNAseq_analysis

Dataset and analysis of Aedes aegypti expression profiles following infection with dengue or RVF viruses

Reproductibility

Analysis and figures can be generated using the following command on an unix terminal

git clone https://github.com/loire/CCS_RNAseq_analysis
cd CCS_RNAseq_analysis
Open analyse.rmd with Rstudio to knit the html or pdf report and generate tables and figures  

Dependencies

R packages: tidyverse, ggrepel,edgeR

Material and methods

• 30 samples
  • 12 biological samples (3 replicates each)
    • RVF 24H
    • RVF 6 days
    • Dengue 24H
    • Dengue 6 days
  • 18 controls (mock community; 3 replicates);
    • "water" (mockA), inactivated viruses (mockB), stress inducing media mockC))
    • 24h and 6 days

Samples are described in file Data/sample.csv

Library construction and sequencing have been performed by Montpellier Genomix

Bioinformatic pipeline

MGX contribution

• fastq files were mapped with bowtie2 on Aedes aegypti genome and transcripts raw abundance inferred with Tophat2 pipeline.

Raw transcripts abundance are reported in in file Data/Raw_Counts_RNA-Seq_CetreSossah.txt