The human cytoplasmic dynein interactome reveals novel activators of motility

This excel file contains all of the mass spectrometry data referenced in the manuscript. The first blue tab corresponds to the Flag immunoprecipitation experiment in Figure 1B. The second blue tab contains the dynein core subunits detected in the Flag immunoprecipitation experiment, corresponding to Figure 1C. The purple tab contains all mass spectrometry data related to Figure 2. The pink tabs contain all of the dynein/dynactin interactome mass spectrometry data. This data was used to generate Figure 3C. The green tabs contain all of the activator interactome mass spectrometry data. This data was used to generate Figure 6 and Figure 6—figure supplement 1. ‘NT’ and ‘CT’ indicate that the BioID tag was on the N-terminus or C-terminus of the full-length protein, respectively.

This excel file contains the mass spectrometry data that was used to generate Figure 2C (second tab) and 2D (first tab).

The blue tabs contain the BioID interactome data for IC1, IC2, LIC1, LIC2, TcTex, RB, and p62. Only the data for dynein and dynactin subunits and known (BICD2, HOOK1 and HOOK3) and suspected (BICD1) activators are shown. The blue tab titled ‘mapping color code’ lists the dynein and dynactin subunits enriched in the BioID experiments and graphically displayed in Figure 3C. Shading indicates enrichment value: light gray (2–3 fold) or dark gray (≥3 fold), p<0.05 (Student’s two-tailed t-test). The entire datasets can be found in Supplementary file 1 (pink tabs in Supplementary file 1). The pink tabs in this excel file contain all of the significant hits from each BioID tagged dynein and dynactin subunit. Significance was defined as >3 fold enrichment, p-values<0.05 (Students two-tailed t-test), and average spectral counts > 2. This data was used to generate the network shown in Figure 3—figure supplement 1. The pink tab titled ‘core hits’ lists the gene names for all hits, specific hits (unique to each tagged subunit), and hits shared by at least two datasets, for the dynein and dynactin BioID tagged subunits. The pink tab titled ‘core Venn’ contains the output from the Venn analysis (http://bioinformatics.psb.ugent.be/webtools/Venn/) of the dynein and dynactin core subunit interactomes used to generate the network shown in Figure 3—figure supplement 1. Proteins found in only one dataset are listed in the excel file, but not shown in the network.

The green tabs contain all significant hits from the NT and CT BioID tagged activator datasets. Significance was defined as >3 fold enrichment, p-values<0.05 (Students two-tailed t-test), and average spectral counts > 2. The blue tab titled ‘NT hits’ lists the gene names for all hits, specific hits (unique to each tagged activator), and hits shared by at least two datasets, for the NT-activator BioID tagged subunits. The blue tab titled ‘NT Venn’ contains the output from the Venn analysis (http://bioinformatics.psb.ugent.be/webtools/Venn/) of the NT activator interactomes used to generate the network shown in Figure 6B. Proteins found in only one dataset are listed in the excel file, but not shown in the network. The blue tab titled ‘white spheres NT’ highlights (in grey) the four hits that were shared by an activator from each activator family (i.e. BICD, HOOK, and NIN). The orange tab titled ‘CT hits’ lists the gene names for all hits, specific hits (unique to each tagged activator), and hits shared by at least two datasets, for the CT-activator BioID tagged subunits. The orange tab titled ‘CT Venn’ contains the output from the Venn analysis (http://bioinformatics.psb.ugent.be/webtools/Venn/) of the CT activator interactomes used to generate the network shown in Figure 6B. Proteins found in only one dataset are listed in the excel file, but not shown in the network. The orange tab titled ‘white spheres CT’ highlights (in grey) the 21 hits that were shared by an activator from each activator family (i.e. BICD, HOOK, and NIN). The pink tabs contain data that contrast all of the activator hits, combining the NT and CT datasets. The pink tab titled ‘NT-CT combined hits’ contains the gene names that are specific for each termini of each activator or shared between any dataset. The pink tab titled ‘NT-CT combined Venn’ contains the output from the Venn analysis (http://bioinformatics.psb.ugent.be/webtools/Venn/) of all activator interactomes used to generate the network shown in Figure 6—figure supplement 1.

This excel file contains gene ontology analyses using the ‘cellular component’ option (GO, geneontology.org). The GO terms with p-values<0.05 are shown for hits that were shared in at least three C-terminal BioID datasets; C-terminal hits that were specific to BICD2, HOOK1, HOOK3, NIN, and NINL; and C-terminal hits that were shared by activator family members BICD1 and BICD2, HOOK1 and HOOK3, and NIN and NINL.