Fig. 7

Investigation into outer segment phagocytosis (OSP) regulators in rab28 KO retinae (A) Time course highlighting sample collection time (red x) in relation to phagosome level fluctuation (B) Heat map representing differentially expressed proteins at ZT 4, ZT 9, or ZT 17 in 2 months post fertilization rab28 KO illustrating proteins significantly upregulated (in red) or downregulated (in green), given a –log p-value cut-off of ≥1.3. Student's t test was used for statistical analysis. (C) Table of 21 proteins derived from the 52 candidate OSP regulators (Figure 6) that have a statistically significant interaction, indicating that for these proteins, the relationships between group (rab28 KO vs. sibling) and log-transformed LFQ intensity depends on Zeitgeiber time (ZT 4, ZT 9, and ZT 17) as determined by a two-way anova. (D) Table of 21 candidate OSP regulators disrupted in rab28 KO documenting in more detail the specific time points altered. The difference in the log-transformed LFQ intensity between the rab28 KO and sibling group, their corresponding lower and upper confidence intervals (LCI and HCI) and the p-value indicating if this difference is significant at each time point respectively is shown. Colored boxes indicate when the p-value for the pairwise t test determines that there is a statistically significant difference between log-transformed LFQ intensity for rab28 KO versus sibling; orange- ZT 4 and ZT 17, yellow- ZT 4, blue ZT 9, green-ZT 17. (E–I) Box and whisker plots showing the log-transformed LFQ intensity of the known OSP-associated proteins Calreticulin, Rab7a, Dynamin-1-like protein, Parkinson disease protein 7 and Rp2 at ZT 4, ZT 9 and ZT 17, highlighting significant differences between wild-type siblings (sibling) and rab28 KO (mutant) at specific time points