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HTS statistics. (A) Sample name, total number of reads, percent of reads mapping, read depth (# mapped reads/Drosophila transcriptome size (30.1 Mba)), percent unique and percent non-unique reads are shown for technical triplicates of each sample. A Studentâ s T-test was used to determine if the observed differences in percentages of non-uniquely mapping reads between samples was statistically significant. Corresponding p values are shown in the last column. (B) Total number of reads and percent or reads mapping when zero mismatches are allowed (left) and one mismatch is allowed (right) for three technical triplicates and one biological replicate (BR) of each sample. (PDF 54 kb)

Taqman assays and primers. Taqman assay ID #s and targets are shown in the top table. Targets of hp and Tn primers are shown in the middle table together with their sequences, position targeted within the Tn and references to their original use. Control GAPDH primers and primers used to assess sop RNA misprocessing are shown in the bottom table. (PDF 67 kb)

Esi1/2 precursors are polyadenylated. Polyadenylation status of CG44774 (Esi1) and CR18854 (Esi2) were assessed as described in [17]. These RNAs are more enriched in the Poly(A)â +â fraction than the polyadenylated Actin mRNA. Non-polyadenylated 18S rRNA is enriched in the poly(A)- fraction. (PDF 29 kb)

Work flow for high throughput sequencing and small RNA analysis (SMACR). (A) Drosophila cells were individually depleted of Dcr2, CPSF73, Symplekin, and GFP (or LacZ). An additional fifth sample was untreated. The untreated and GFP samples represent controls. RNA was isolated from each sample and fractionated into RNAs > than 200 nts and RNAs

Physical characteristics of miRNAs, Tn- and hp-derived esiRNAs in Symplekin, CPSF73, Dcr2 knockdown and control samples. Mapped siRNAs were sorted by type and filtered by size (21-24 nts) (A), 3â base (B), and 5â base (C) for each sample. The abundance of normalized read counts in each category was then summed and the percentage of each individual category was calculated for all samples. Percentages for each category were then plotted. (PDF 208 kb)

Immunofluorescence shows Dcr2 in the nucleus. Immunofluorescence of Drosophila culture cells with anti-Dcr2 and anti-Symp antibodies shows both Dcr2 and Symplekin co-localizing with the DAPI stained nucleus. (PDF 130 kb)

Immunofluorescence shows Dcr2 in the nucleus. Immunofluorescence of Drosophila culture cells with anti-Dcr2 and anti-Symp antibodies shows both Dcr2 and Symplekin co-localizing with the DAPI stained nucleus. (PDF 130 kb)