For all other analyses, specific peaks were considered to be supported by chimeras if chimeras from high-confidence small RNAs (see miRDeep2) were observed in that maximum location in any library (Scheel et al., 2017). lengths, 6mer seed (six_mer), and 6mer target sequence (six_mer_target). Normalized counts in reads per million mapped (RPM) by sample type (counts_norm); AGO1 versus AGO2 association in Aag2 cells or whole mosquitoes (log2Aag2AGO1overAGO2, log2aegyptiAGO1overAGO2) are indicated. The same was carried out for chimeras that contained small RNAs; RPM of chimeras that remapped to the AaegL5 genome (norm_chimera), and AGO1 versus AGO2 association (log2Aag2AGO1overAGO2_chimera, log2aegyptiAGO1overAGO2_chimera) is definitely indicated. Quantity of libraries where chimeras were present is definitely demonstrated by sample type for each small RNA (BC_chimera). For novel small RNAs, miRDeep2 output parameters are demonstrated (best miRDeep2_score, estimated_probability_smallRNA_is definitely_true_positive, signficant_Randfold, unique precursor_coordinate). Unique estimated probabilities the small RNA is definitely a true positive are shown for each sample in which the small RNA was annotated, separated by ;. Precursor coordinates are shown in the format chromosome:start_stop:strand, and multiple unique precursors are separated by ;. Individual small RNAs sharing a 6mer seed in were grouped into IGFBP2 families (aae_smallRNA_family); small RNAs sharing a 6mer with known miRNAs in other species are shown (cqu_related_miRNA_family = = previously un-annotated. Pomalidomide-C2-NH2 hydrochloride NIHMS1683502-supplement-Table_S4.xlsx (131K) Pomalidomide-C2-NH2 hydrochloride GUID:?8B665237-01C4-44EB-8CDC-6B09E9E8CCF0 Table S5: Table S5. AGO-CLIP RNAi network map, related to Figures 3C7. (provided as an Excel file) High-confidence small RNAs linked with high-confidence AGO1 and AGO2 targets in cells and mosquitoes. The small RNA family, a group of small RNAs that share the same 6mer target, is usually indicated (aae_smallRNA_family), followed by the target type (predicted 6mer, predicted 7mer-A1, predicted 7mer-M8, predicted 8mer, chimera); target peakID in the format chromosome:start_stop:strand; target genomic coordinates for the AaegL5 assembly (chromosome, start, end, peak width, strand); target genomic annotation, geneID, and transcriptID; the sample(s) in which this peak was a high-confidence target, separated by ;; and the sample(s) in which chimeras were observed, separated by ;, if applicable. Note that peaks may be supported by multiple small RNAs; = previously un-annotated. NIHMS1683502-supplement-Table_S5.xlsx (1.2M) GUID:?8A812995-1DD8-407A-8300-D94339D1D76D Table S6: Table S6. All Pomalidomide-C2-NH2 hydrochloride fgsea results for cells and mosquitoes, related to Physique 4. (provided as an Excel file) Leading edge genes are the genes responsible for observed GO term enrichment (Leading Edge Gene ID). GO terms containing the exact same leading edge gene sets were collapsed (each individual GO term is usually separated by a comma). The number of genes present in the data for each GO term is usually indicated (size). The p-value and normalized enrichment score (NES) for each set Pomalidomide-C2-NH2 hydrochloride of GO terms is also indicated, with positive NES values reflecting AGO2-enriched GO terms and unfavorable values indicating AGO1-enriched GO terms. NIHMS1683502-supplement-Table_S6.xlsx (301K) GUID:?C5FF3920-1584-42B5-B9D8-9ED1DBE4E49B Table S3 [1: Table S3. Processing and alignment statistics for all those CLIP datasets, related to Figures 3C7. (provided as an Excel file) Experiment, antibody, lysate, cloning procedure, and index are indicated by sample for all those sequencing libraries included in this study. Uncollapsed and collapsed numbers indicate processed reads. Collapsed reads mapping to the genome (AaegL5_mapped), and the numbers (AaegL5_remapped_chimeras) and percentages (AaegL5_chimera_percent, normalized to the number of AaegL5 mapped reads) of chimeric reads made up of small RNAs where the target portion of the RNA remapped to the AaegL5 genome are shown. Collapsed total reads mapping to the cell fusing agent virus genome (CFAV_mapped), Phasi Charoen -like virus genome Pomalidomide-C2-NH2 hydrochloride (PCLV_mapped), and Culex Y virus genome (CLY_mapped) are also shown. The percentage of total virus-mapped reads (CFAV_percent, PCLV_percent, CLY_percent) and percentage of likely vsiRNAs (18C24nt; CFAV_vsiRNA_percent, PCLV_vsiRNA_percent, CLY_vsiRNA_percent) for each virus is also shown, normalized to the number of AaegL5 mapped reads. PCLV and CLY columns include reads that mapped to all segments. NIHMS1683502-supplement-Table_S3__1_.xlsx (25K) GUID:?ED69A673-42D5-4241-B69E-869805AA0852 Data Availability StatementAll full-length western blots and gels for mass spectrometry are available in the Supplementary Information. Experimentally validated AGO transcript/protein isoforms were deposited in GenBank under accessions: “type”:”entrez-nucleotide”,”attrs”:”text”:”MW035627″,”term_id”:”1929628176″,”term_text”:”MW035627″MW035627-“type”:”entrez-nucleotide”,”attrs”:”text”:”MW035631″,”term_id”:”1929628184″,”term_text”:”MW035631″MW035631. The code used in this study.