Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense
1 Department of Statistics, Colorado State University, Fort Collins, Colorado, 80523, USA
2 Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA
3 Microbiology, Immunology, and Pathology Dept, Colorado State University, Fort Collins, Colorado, 80523, USA
4 Arthropod-borne Infectious Diseases Laboratory; Colorado State University, Fort Collins, Colorado, 80523, USA
5 Life Technologies, Foster City, CA, 94404, USA
6 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
BMC Microbiology 2011, 11:45 doi:10.1186/1471-2180-11-45Published: 28 February 2011
Additional file 1:
Additional viRNA profiles. A. sRNA reads from representative libraries of un-infected controls show non-specific alignment to the DENV2 genome. Panels from left to right indicate, 2, 4, and 9 dpi, respectively. Top panel shows count distribution along DENV2 genome for a representative library at each timepoint. Bottom panel shows mean sRNA distribution by size. Blue and red bars indicate sense and anti-sense sRNAs, respectively. B. viRNA WebLogos. viRNAs from a representative 9 dpi DENV2-infected cohort were separated by size group and subjected to WebLogo sequence alignment http://weblogo.berkeley.edu/ webcite to identify the relative nucleotide frequency at each position. About 20,000 reads were analyzed for the combined categories. C. 24-30 nt piRNAs are more abundant in DENV2-infected samples. Total mean transcriptome-mapped reads of un-infected and DENV2-infected libraries categorized by sRNA size group. Blue and red bars indicate sense and anti-sense viRNAs, respectively.
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Additional file 2:
Host sRNA Profile Summary Tables. Summary data categorized by mapped read orientation and sRNA size group. 'Summary' page shows total sRNA reads in pooled libraries for each condition tested. ''Transcripts' shows the number of targets remaining after removing low-abundance (<10 reads) and flagged candidates. "Flagged" segments are those for which a replicate accounted for 70% or more of the total reads; these were deleted from the final analysis. 'Enriched' and 'Depleted' indicate the number of targets showing significant changes in DENV2-infected pools over controls. Significance was determined using the edgeR exact test, and a Benjamini-Hochberg cut-off of 0.05 was used to adjust for multiple testing and control the false discovery rate. The following pages list raw sRNA count data for each target transcript at 2, 4, or 9 dpi. 'DayX sense' shows differential enrichment data for host sense strand sRNAs across all libraries collected at X dpi. Other pages show similar sRNA profiles for anti-sense and sense strand sRNA reads at the indicated collection time. 'Category', indicates target functional category described in Figure 3 legend. 'logFC', log2 fold change in DENV-infected versus control for all sRNAs; 'F_pval', p value of exact test, 'F_FDR', FDR for summed sRNAs. Day2 ncRNA Table shows unique tRNAs represented in the enriched sRNA profiles at 2 and 4 dpi. qRT-PCR Primers Table shows primers used in analysis shown in Figure 3F.
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Additional file 3:
Targets sharing sRNAs from different size categories. Venn diagram shows the number of targets that share sRNAs of different size groups for 2 and 4 dpi.
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