Supplementary Methods and Figures

Supplementary Methods and Figures.

This file contains Supplementary Methods and Supplementary Figures 1-12 with legends and associated references (Adobe Acrobat document, 13 MB).

Supplementary Table 1.

This table lists the primary data for the virus capsid/autophagosome colocalization screen. Shown are the z-scores for each replicate for each gene in the Dharmacon siRNA library. “NA” denotes insufficient numbers of green or red puncta per cell or total number of cells per well for analysis (MS Excel spreadsheet, 4656 KB)

Supplementary Table 2.

This table lists the data for the virus capsid/autophagosome colocalization confirmation screen, using a customized library (from Dharmacon) composed of individual siRNAs from the pool of 4 siRNAs targeting each gene that scored “positive” in the primary co-localization screen. Genes with p-values of <0.05 for 2 or more individual siRNAs were considered confirmed colocalization hits. “NA” denotes insufficient numbers of green or red dots per cell or total number of cells per well for analysis (MS Excel spreadsheet, 127 KB).

Supplementary Table 3.

This table lists the results for each individual siRNA from a pool of 4 targeting each gene that scored positive in the primary screen for viral capsid/autophagosome colocalization, with respect to whether they scored positive in the confirmation screen of viral capsid/ autophagosome colocalization (C) screen, the secondary screen for survival of virus-infected cells (S) and the secondary screen for Parkin-mediated mitophagy (M). siRNA sequences are listed in column J. For each siRNA, this table also lists the number of 7-8mer miRNA seed sequences (positions 2-8 on mature miRNA) contained in each siRNA oligo (column K), the identity of such seed sequences (columns L-0), and the specific miRNAs that contain the seed sequences (columns P-S). The confirmed siRNAs in each screen are not enriched for siRNAs containing miRNA seed sequences (P=0.95 for colocalization screen; P=0.71 for cell survival screen; and P=0.97 for mitophagy screen) (MS Excel spreadsheet, 195 KB).

Supplementary Table 4.

This table lists the predicted targets (identified using TargetScan) for each miRNA seed sequence listed in Supplementary Table 3 (MS Excel spreadsheet, 302 KB).

Supplementary Table 5.

This table lists the molecular function and biological process categories from Panther and Gene Ontology, and protein class and pathway assignments from Panther for the siRNA hits in the viral capsid/ autophagosome colocalization screen. Clusters listed correspond to graphical representation in Supplementary Figure 3a (MS Excel spreadsheet, 36 KB).

Supplementary Table 6.

This table lists the data from the cell survival screen, using a using a customized library (from Dharmacon) composed of individual siRNAs from the pool of 4 siRNAs targeting each gene that scored “positive” in the primary colocalization screen. Genes with p-values of <0.05 for 2 or more individual siRNAs were considered to be confirmed cell survival factors during viral infection (MS Excel spreadsheet, 36 KB).

Supplementary Table 7.

This table lists the data from the mitophagy screen, using a customized library (from Dharmacon) composed of individual siRNAs from the pool of 4 siRNAs targeting each gene that scored “positive” in the primary colocalization screen. Genes with p-values of <0.05 for 2 or more individual siRNAs were considered to be confirmed mitophagy factors (MS Excel spreadsheet, 127 KB).

Supplementary Table 8.

This table includes the data in Figure 2a of the main text, with additional details for each gene including Locus ID, Gene Accession numbers, and Gene Annotations from Panther Molecular Function (MF), Panther Biological Process (BP), and UniProt (MS Excel spreadsheet, 112 KB).