Supplemental Figures:

Figure S1. Analysis of endo-siRNA targets in different microarray datasets. The

percentage of each array dataset that were predicted endo-siRNA targets according to the

Ambros dataset (Lee et al. 2006) was plotted [(number of endo-siRNA targets in

microarray dataset / total genes in microarray dataset) * 100]. Data are also presented for

the datasets after parsing into upregulated and downregulated genes. Additionally, the

genes common to two or more of the lists of upregulated genes were also analyzed (∩

indicates intersection between datasets). The random analysis represents the average

value using ten independently generated random lists of genes (see Experimental

Procedures).

Figure S2. Chromosomal location and strand orientation of all misregulated genes in the

dcr-1(-/-) dataset. Horizontal black line depicts chromosome. Vertical bars indicate

misregulated genes, depicted above and below the chromosome to denote opposite strand

orientations.

Figure S3. Figure of significant GO terms that are under-represented among

misregulated genes in animals that lack dcr-1, rde-4 or rde-1. See legend to Figure 3 for

additional details.

Supplemental Table Legends

Table S1

Datasets of genes determined to be misregulated by microarray analyses of dcr-1(-/-),

rde-4(-/-), and rde-1(-/-) mutants. A separate worksheet was created for each curated list

of genes and shows the Affymetrix probeset ID, the fold change, and direction of

misregulation. A separate worksheet was also included for analyses of the intersections

between the three datasets. In addition, for each microarray analysis the complete output

from the microarray analysis suite (GeneSifter) is provided as a separate worksheet.

Table S2

Analyses of PicTar predicted miRNA targets in the dcr-1(-/-), rde-4(-/-), and rde-1(-/-)

datasets. The accumulated list of PicTar predicted miRNA targets (cePicTar) that was

generated from data obtained from the PicTar website (http://pictar.bio.nyu.edu/cgi-

bin/new_PicTar_nematode.cgi?species=nematode) is given in column A of the worksheet

“cePicTar”. A description of how the cePicTar list was generated, as well as the raw

numbers from the miRNA analysis are presented in the worksheet “methods.” Column A

of worksheet “PicTar AND dcr upregulated” lists the subset of all PicTar predicted

miRNA targets that are upregulated in the dcr-1(-/-) dataset. The PicTar predicted let-7

targets are listed in column A of the worksheet “PicTar let-7” with the dcr-1(-/-)

upregulated genes highlighted in blue.

Table S3

Analysis of the overlap between previously published infection study datasets (Huffman

et al. 2004; O'Rourke et al. 2006; Shapira et al. 2006) and dcr-1(-/-), rde-4(-/-), and rde-

1(-/-) datasets. The lists of genes used for each infection study microarray are presented

in worksheet “immunity lists” with the upregulated and downregulated genes denoted in

red or green, respectively. The quantitative analysis of overlap between the microarray

datasets are presented in the worksheet “intersection of microarrays.” Shown in Section

A are the number of misregulated genes that are common to both of the datasets being

compared. The number of genes expected to be common as a result of random chance is

shown in Section B. The ratio of observed (Section A) / expected (Section B) is presented

in Section C. Additionally, the genes used to determine misregulated members of families

linked to innate immunity are listed in worksheet “innate immunity families” (columns

N-AH). The number of family members misregulated in each of the datasets analyzed

(columns B-J) is presented along with the details of the analysis.

Table S4

This dataset shows the lists submitted to Fatigo+ for analysis. For each mutant animal

analyzed, column A (init_genes 1) corresponds to the genes misregulated ≥ 1.5 fold and

column B (init_genes 2) corresponds to the remainder of genes on the array.

Table S5

This dataset includes the complete Fatigo+ analysis for each mutant animal. Values

reported in columns C and F indicate the number of genes found with the specified GO

term among the ≥ 1.5 fold misregulated genes (column C) or the remainder of the genes

on the array (column F, total genes on the array excluding those on the ≥ 1.5 fold list).

Values in columns C and F were divided by the total number of genes with annotation at

the specified ontological level to determine the percentage values shown in columns D

and G. For the percentage values plotted in Figures 3 and S3, the total genes at the

specified ontological level are as follows. dcr-1, ≥1.5 fold: level 3, 437 (mf), 465(bp) and

231(cc), and level 4, 377(mf), 432(bp) and 159(cc); array minus ≥ 1.5 fold: level 3,

5219(mf), 5346(bp) and 2906(cc), and level 4, 4432(mf), 5079(bp), and 1976(cc). rde-4,

≥1.5 fold: level 3, 140(mf), 130(bp), 42(cc), and level 4, 119(mf), 109(bp) and 28(cc);

array minus ≥1.5 fold: level 3, 5515(mf), 5678(bp), 3090(cc); level 4, 4684(mf),

5397(bp) and 2108(cc). rde-1, ≥1.5 fold: level 3, 25(mf), 25(bp), 10(cc) and level 4,

23(mf), 25(bp), 8(cc); array minus ≥ 1.5 fold: level 3, 5629(mf), 5782(bp) and 3127(cc)

and level 4, 4780 (mf), 5482 (bp), 2128 (cc).