Extended Data Fig. 5: Rhi binding upon E(z)-kipf double knockdown.
a-d, MA plot showing counts per TE (black) in sRNA-seq libraries from ovaries of germline (a) E(z) KD versus control, (b) E(z)-kipf dKD versus control, (c) E(z)-kipf dKD versus E(z) KD, and (d) E(z)-kipf dKD versus kipf KD. Sense and antisense piRNAs are shown separately and TEs with padj<0.05 and >4x fold change are shown in red (DESeq2, two-sided Wald test). e, Boxplots showing changes in piRNAs mapping uniquely to genomic 1 kb bins within heterochromatin, euchromatin or indicated piRNA clusters (n refers to the number of 1 kb bins for each category). Signal shown as a log2-ratio between the indicated KD and its respective control (average of 1-3 biological replicates). P-values were calculated using a two-sided paired Wilcoxon signed-rank test for >2-fold changes. Boxplots show median (central line), interquartile range (IQR, box), and minimum and maximum values (whiskers, at most 1.5*IQR). f, Scatter plot depicting normalized uniquely mapping piRNA levels in 1 kb bins in ovaries with nos-Gal4 driven E(z) knockdowns versus control (average of two replicates each). g, Scatter plot depicting normalized uniquely mapping piRNA levels in 1 kb bins in ovaries with nos-Gal4 E(z)-Kipf dKD compared to nos-Gal4 driven w knockdown (average of two replicates each). h, Same as d but comparing E(z)-kipf dKD to nos-Gal4 driven E(z)-w dKD (average of two replicates each). i, Same as d but comparing E(z)-kipf dKD to nos-Gal4 driven kipf knockdown (average of two or three replicates each). j, Immunofluorescence staining showing Rhi expression and localisation in nurse cell nuclei upon the indicated shRNA and nos-Gal4 driver combination (scale bar: 5 μm). Data are representative of n > =3 independent experiments.
