Computational protocol: Strain Variation in the Transcriptome of the Dengue Fever Vector, Aedes aegypti

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Protocol publication

[…] RNA-seq data for the CTM and Rex-D strains are deposited at the NCBI Gene Expression Omnibus under accession number GSE32074. RNA-seq data for the LVP strain are available under the accession number GSE24872 (). Sequence reads were mapped to the LVP reference genome with Bowtie (), allowing a maximum of two mismatches and with the –m option, which returns only reads with a single best match in the genome ().Differential transcript accumulation levels among conditions were assessed by the likelihood ratio test implemented in DEGseq (), after accounting for the different total gene counts of each library, and at a P value of 0.001 with a false discovery rate of 0.1% (). Use of the modifier “significant” in the following text implies that accumulation values met the statistical criteria.The reference file containing transcript annotation information and used in DEGseq was generated by converting a GTF annotation file obtained through http://metazoa.ensembl.org/ to the format (refflat) accepted by DEGseq and represents gene-build AaegL1.2. Function parent attribution of the sequenced transcripts is based on the Ae. aegypti database AegyXcel (http://exon.niaid.nih.gov/transcriptome.html#aegyxcel). Transcripts accumulated differentially among samples were visualized in the Ae. aegypti protein network () with the use of Cytoscape_v2.7.0 (http://www.cytoscape.org/). Metabolic pathways were analyzed by LinkinPath (), which accepts a maximum of 5000 sequences per session and the color of each group of sequences is assigned automatically. […]

Pipeline specifications

Software tools Bowtie, DEGseq
Databases GEO
Application RNA-seq analysis
Organisms Aedes aegypti
Diseases Dengue, Infection, HIV Infections
Chemicals Amino Acids, Carbohydrates