Processing/mapping/peak matrix code for AGO targets (there are no graphical outputs): link
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PCAs of all unfiltered samples (Figure S3D), filtering of high-confidence AGO targets (data underlying Figures S3A-C), and PCAs of high-confidence targets in cells and whole mosquitoes (Figures 4G and 4J)
fgsea of high-confidence gene targets associated with AGO1 or AGO2 (Figures 4H, 4I, 4K, 4L and Table S6)
genic annotation of high-confidence targets (Figures 4C-4F)
Venn diagram of gene targets of AGO1 and AGO2 in cells and whole mosquitoes (Figure S3E) and Venn diagram comparing gene targets from Zhang et al., 2017 (Figure S3H)
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Processing/miRDeep2 discovery/quantification and filtering to obtain high-confidence novel small RNAs
Abundance of high-confidence known miRNAs and novel small RNAs in AGO1 and AGO2 (Figures 4A and 4B)
Length distribution of high-confidence novel small RNAs and known miRNAs associated with AGO1 or AGO2, in cells or whole mosquitoes (Figure S2A and S2B)
Venn diagrams showing presence of AGO1-associated high-confidence known (Figure S2C) or novel (Figure S2D) miRNAs in cells compared to whole mosquitoes
Chimera processing to identify reads containing small RNAs and targets (there are no graphical outputs): link
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Enrichment of abundant known (Figures 5A and S4A) and novel miRNAs (Figures 5B and S4B) in sequences in AGO1 peaks
Enrichment of known miRNAs that have similar abundances as the most abundant novel miRNAs (Figures S4C and S4D) in sequences in AGO1 peaks
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Quantification of chimera abundance, and comparison of high-confidence known miRNAs and novel small RNAs by overall abundance, or by chimera abundance (Figures 5D, S4F, S6C, and S6E)
Table S4 formatting, naming of novel small RNAs, and selecting the most abundant small RNA families
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Scatterplots showing the correlation between miRNA families and their targets, and inset pie charts showing the percentages of high-confidence miRNAs by class (Figures 5C and S4E) Genic annotation of high-confidence AGO2 targets of abundant AGO2-loaded small RNAs in cells and mosquitoes (Figures S3F and S3G)
Table S5 formatting
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Read coverage over 3’UTRs for AGO1 (Figure 5E and S4G) and AGO2 (Figure 6A)
Frequency of chimeras and predicted 6mers over 3’UTRs for AGO1 (Figures 5F and S4H) and AGO2 (Figures S6B and S6D)
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Mapping all samples to repeat features and visualization of repeat feature families with significantly higher percentages of mapped reads in AGO2 libraries versus paired IgG controls (Figure 6B)
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Mapping all samples to endogenous viral elements (EVEs) and visualization of EVE families with significantly higher percentages of mapped reads in AGO2 libraries versus paired IgG controls (Figure 6C)
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Quantification of size and strand bias for Ae. aegypti-mapped (Figures S5C and S5D) or CFAV-mapped (Figure 6D) short reads, from AGO1 or AGO2 libraries
Click link to see: Reprocessing of small RNA-seq data from Aag2 cells from:
Ma et al., 2021; PRJNA610833
Miesen et al., 2016; PRJNA310830
Haac et all., 2015; PRJNA272825
Graphs of small RNA length and strand bias on persistent viruses infecting Aag2 cells from small RNA-seq or CLIP data (Figures S5F-S5H)
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Enrichment of abundant novel esiRNA sequences in AGO2 peaks (Figures 6F and S6A)
Histogram showing the number of perfect 18mer targets from the same esiRNA family found on AGO2-bound transcripts (Figure S6F)
Putative AGO2 specificity motifs (Figures 6G and S6G)
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Selection and normalized expression of mosquito ovarian miRNA targets (Figures 7A-7C) or control miRNA targets (Figures S7A and S7B), or their relative expression in all individual mosquito tissues from Matthews et al., 2016 (Figure S7C)
Selection of targets by type for abundant novel mosquito esiRNAs or AGO2-associated known miRNAs, their relative expression in all individual mosquito tissues from Matthews et al., 2016 (Figure S7D), or their normalized expression in ovaries compared to all tissues (Figures 7E and 7F)
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Reprocessing of small RNA-seq data from Akbari et al., 2013 to quantify novel esiRNA expression in ovaries (Figure 7D)