Computational protocol: Parallel Epigenomic and Transcriptomic Responses to Viral Infection in Honey Bees (Apis mellifera)

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Protocol publication

[…] Transcriptome sequencing reads were preprocessed using Illumina HCS 1.1 software. We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10. The transcriptome sequencing reads were aligned to the most recent honey bee genome assembly (Amel_4.5) [] using Tophat[]. Aligned read counts were imported into R statistical software (http://www.r-project.org). Genes with low read counts (less than 5 reads per gene) were removed. The data was normalized using a trimmed mean of M-values (TMM) method []. The DESeq package in R statistical program was used to identify significantly differentially expressed genes [].For the gene ontology (GO) analysis, D. melanogaster orthologs of the differentially expressed genes were uploaded to DAVID Bioinformatics Resources 6.7[]. The overrepresented GO terms of differentially expressed genes during viral infection were determined using a background list of all genes expressed among the samples. To refine the list of GO terms, the significant terms (FDR < 0.05) that were generated using DAVID Bioinformatics Resources were imported into REVIGO [], which clusters the GO terms using semantic similarity measures. […]

Pipeline specifications

Software tools TopHat, DESeq, DAVID, REViGO
Application RNA-seq analysis
Organisms Apis mellifera, Israeli acute paralysis virus, Homo sapiens, Viruses, Human poliovirus 1 Mahoney
Diseases Infection, Virus Diseases