Download Supplementary Table Legends

Supplementary Table Legends
Table S1. Peptide ID Reproducibility In BioID Biological Replicates. Related To
Figure 1.
(top) R2 values for each bait protein in ciliated and non-ciliated conditions. (bottom)
Counts observed in pool A versus pool B for all unique peptides (identified in both pool
A and pool B; TPP>0.85). Red circles and blue crosses depict results in cycling or
ciliated cells, respectively. Correlation formula and R2 values are indicated at the top
right of each graph, and summarized in the table (top right).
Table S2. Network Attributes. Related To Figures 1-7.
Details of the non-ciliated and ciliated interactomes (see tabs, and use ‘filtering’ option
on each column heading to select lists of interest). Interactor and PxI attributes (in tabs)
used for all network map construction in the manuscript, and SAINT scores, and
MaxSpec counts are included. Bait-Bait interaction data used to build Figures 1C-D is
also detailed here (‘bait-bait PxI’ tab).
Table S3. CCDB. Related To Figures 1-2, S1-S2.
CentrosomeDB (Alves-Cruzeiro et al., 2014) and The SysCilia Gold Standard (SCGS)
Version 1 (vanDam et al., 2013) were used as sources to assemble a master reference
list of 1554 proteins (column 3) with previous evidence for centrosome (column 1) or
cilium association (column 2), which is referred to as the centrosome and cilium
database, CCDB.
Table S4. Flag-IP MS Comparison With BioID. Related to Figures S1D-E.
Details of FLAG-IP MS results and their side-by-side comparison with BioID results for
the same subset of baits (see tabs within worksheet). Individual preys and their
presence or absence with both methods, along with their SAINT scores are tabulated.
See summary tab for the calculations presented in Figures S1D-E.
Table S5. Comparison Of Firat-Karalar et al. Versus This Study. Related To Figure
S1F.
Details of Firat-Karalar study, taken from (Firat-Karalar et al., 2014), and their side-byside comparison with BioID results for the same subset of baits (see ‘ID’ tab). Individual
preys and their presence or absence with both methods, are tabulated. See summary
tab for the calculations presented in Figure S1F.
Table S6. “Clustergram” Group Information. Related To Figure 2.
Each interactor group depicted in Figure 2 is detailed, along with associated GO
enrichment analysis (DAVID ontology Enrichment Clustering).
Table S7. Sub-Appendage Localization Measurements. Related To Figure 3D.
Average fitted line profile distance in nm, between protein of interest and controls
(CEP164, NIN), and between controls. See Suppl. Exp. Proc. for details. Averages of
at 3 independent measurements shown.
Table S8. Detailed Functional Screen Results. Related To Figure 4.
All replicate z scores from screens, for non-ciliated (500 genes) and additional 35 genes
for ciliated conditions. Summary tab indicates whether a given gene was hit in the
respective column category. Use the ‘filter’ feature in Excel to navigate specific queries.
4 specific parameters from the satellite screen (‘PCMi’, ‘PCMo’, ‘CEPi’, ‘CEPo’) and
their directions (‘UP’ or ‘DOWN’) are tabulated (see Suppl. Exp. Proc.). Also, any
change for the combined criterion ‘PCM’ or ‘CEP’ (i.e. any change for that channel) is
also shown. Additional combined categories are ‘Any Sat’ (hit in any satellite
parameter) or ‘Cilia’ (hit in any direction for ciliation), or ‘Any phenotype’. The presence
of the candidate gene in Centrosome or Cilia databases (see Table S3) is also
tabulated. Finally, individual tabs contain all replicate Z-scores, and cell numbers for
each measurement, and ks scores (for the satellite screen only).
Table S9. Hierarchical Clustering Of Centriole baits. Related To Figures 5-6.
Heirarchical clustering as performed by Dot Plot and Heatmap generator
(http://prohitstools.mshri.on.ca/) with default options (Spectral counts, hierarchical
clustering) and just the centriole group of baits. The two clusters used for Figure 5 and
6 are boxed.
Table S10. Differential BioID proximity profiles between ciliated and non-ciliated
conditions. Related To Figures 7A-B.
Detailed interactions between the Tz2 cluster and the Tz1-Core-Peripheral clusters in
non-ciliated and ciliated conditions
Table S11. List of primers, clones, siRNAs, CRISPR guide RNAs, and antibodies
used in this study. Related to Supplemental Experimental Procedures.