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[…] b'samples. The total number of reads for the RNA-seq samples were between 51,231,170 and 53,823,222, and for the BS-seq, the total number of reads for each sample were between 101,423,954 and 102,213,608. Data generated from these studies has been deposited in NCBI\xe2\x80\x99s Gene Expression Omnibus[] and are accessible through the GEO Series accession number GSE65659., 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., To validate the results of the transcriptomic analysis, we repeated the experiment using a new set of bees. Emerging worker bees were collected and fed either viral extracts in a 50% sucrose solution or a 50% sucrose control solution as before. As an additional control, we also included a bee lysate control, using healthy, non-symptomatic bees, that was extensively washed to remove as much of the virus as possible. The groups were reared under the same conditions as before, and monitored hourly for symptoms of viral infection starting 15 hours post infection. All bees were collected 24 hours after treatment. RNA was ' […]

Pipeline specifications

Software tools TopHat, DESeq, DAVID, REViGO
Organisms Apis mellifera, Israeli acute paralysis virus, Homo sapiens, Viruses, Human poliovirus 1 Mahoney
Diseases Death, Infection, Lecithin Cholesterol Acyltransferase Deficiency, Paralysis, Respiratory Paralysis, Virus Diseases, Wiskott-Aldrich Syndrome, Hearing Loss