Supplemental Figure Legends. Supplemental Figure S1. Comparison of the total experimental dataset versus the predicted human proteome, related to Figure 1 ...
Supplemental Figure Legends
Supplemental Figure S1. Comparison of the total experimental dataset versus the predicted human proteome, related to Figure 1. (a) The frequency of each amino acid is compared between the total experimental dataset and an in silico translation of the human proteome. (b) The frequency of biological process gene ontology terms is compared between the total experimental dataset and an in silico translation of the human proteome. Supplemental Figure S2. Analysis of compartment specific degradation for the RDPs from the total experimental dataset, related to Figure 2. The relative fold change in each subcellular fraction for the RDPs detected in the total experimental dataset is shown on the x-axis using the log2 ratio cycloheximide/DMSO (Medium/Light). Error bars show the standard deviation. Supplemental Figure S3. Analysis of the response to MG132, related to Figure 3. (a) The total experimental dataset was analysed to determine the fold change after either cycloheximide, or MG132 treatment, on both K48-linked ubiquitin and ubiquitinated histone H2A. Abundance changes of the total ubiquitin and histone H2A proteins are also shown. The y-axis shows the relative fold change using the log2 normalised ratio for either cycloheximide/DMSO (Medium/Light), or MG132/DMSO (Heavy/Light). Error bars indicate standard deviation. (b) Immunoblotting of total cell lysates of U2OS cells after exposure to either DMSO, cycloheximimde or MG132 for 6 hours. (c) Immunoblotting of total cell lysates from U2OS cells after 24 hours of siRNA knock-down using either a “Jumble” negative control siRNA, a human PRR11 specific siRNA, or a human LaminA/C specific siRNA, (n=3). Arrow head (filled white) indicates the lower PRR11 band and an asterisk marks a nonspecific band. Supplemental Figure S4. Localisation of PRR11 in U2OS cells, related to Figure 5. (a) Immunofluorescence microscopy of asynchronous U2OS cells stained for endogenous
PRR11 (red), vimentin (green) and DNA (blue). White arrows indicate mitotic cells (n=3). Scale bar indicates 10 m. Supplemental Figure S5. Network analysis of the rapidly depleted proteins in each subcellular fraction, related to Figure 6. The analysis of networks within the RDPs from each subcellular fraction using the STRING database. Each protein is represented by a node. Lines between nodes indicate a connection such as experimental interaction (pink), co-expression (black), interaction databases (blue), literature (green), and homology (purple). Kmeans clustering has been used to highlight sub-networks within the RDP dataset with common colouring of these nodes. Networks are shown for (a) cytosol, (b) membrane, (c) nucleus and (d) cytoskeleton.
Supplemental Figure S6. Full scans of blots from Figure 3c. Molecular weight markers are indicated.
Supplemental Figure S1 a
Total Dataset
Predicted Human Proteome
10 9 8
Frequency (%)
7 6 5 4 3 2 1 0 A
b
R
N
D
C
Q
E
G
H
I
L
K
M
F
Percentage of Predicted Human Proteins with GO Term
Amino Acid
10 9 8 7 6 5 4 3 2 1 0 0
1
2
3
4
5
6
7
8
9
Percentage of Proteins in Total Dataset with GO Term
