WBPaper00041163:hly(+)-V-cholerae_induced

The data were processed using Partek Genomics Suite, version 6.4 Partek Inc, St. Louis, MO. The robust multichip averaging algorithm was used to normalize and summarize the probe data into probe set expression values. Analysis of variance, fold-change, and false discovery rate (FDR) calculations were also performed using Partek H Genomics Suite TM version 6.5 (Copyright 2010 Partek Inc., St. Louis, MO, USA). Transcripts showing a corrected p-value of <= 0.05 and fold change <= -1.2 or >= 1.2 were considered differentially expressed between experimental treatments groups. Genes induced over twofold following infection of C. elegans with hly(+) V. cholerae strains.

WBPaper00032062:age_regulated_genes

ANOVA, p < 0.0001. Genes that showed significantly changed expression during aging (ANOVA, p < 0.0001)

WBPaper00032003:ced-1(e1735)_upregulated

The microarray data were subjected to the Robust Multichip Averaging (RMA) Algorithm by using Partek Software (Partek, Inc., St. Charles, Missouri). GeneSpringSoftware9.0(AgilentTechnologies) was used to perform hierarchial cluster analysis. Genes that showed increased expression in ced-1(e1735) comparing with in N2.

WBPaper00062684:pathogen_upregulated_N2

DESeq2 (v.3.1.0), adjusted P-value < 0.05 and fold change >= 2. Transcripts in N2 animals that showed significantly increased expression across all pathogens (S. epidermidis, P. rettgeri, P. aeruginosa, or S. aureus vs. OP50)

WBPaper00062684:pathogen_downregulated_CB4856

DESeq2 (v.3.1.0), adjusted P-value < 0.05 and fold change >= 2. Transcripts in CB4856 animals that showed significantly decreased expression across all pathogens (S. epidermidis, P. rettgeri, P. aeruginosa, or S. aureus vs. OP50)

WBPaper00062684:pathogen_upregulated_CB4856

DESeq2 (v.3.1.0), adjusted P-value < 0.05 and fold change >= 2. Transcripts in CB4856 animals that showed significantly increased expression across all pathogens (S. epidermidis, P. rettgeri, P. aeruginosa, or S. aureus vs. OP50)

WBPaper00062684:pathogen_downregulated_N2

DESeq2 (v.3.1.0), adjusted P-value < 0.05 and fold change >= 2. Transcripts in N2 animals that showed significantly decreased expression across all pathogens (S. epidermidis, P. rettgeri, P. aeruginosa, or S. aureus vs. OP50)

WBPaper00056326:zip-3(gk3164)_upregulated_P.aeruginosa-infected

p < 0.05 Transcripts that showed significantly increased expression in zip-3(gk3164) comparing to in N2, after exposed to P. aeruginosa for 18 hours.

WBPaper00066610:Camptothecin_downregulated_25C_20h

p < 0.01, logFC > 1 or p < 0.01, logFC < -1. Transcripts that showed significantly decreased expression in animals exposed to Camptothecin for 20 hours at 25C.

WBPaper00066610:Camptothecin_downregulated_2C_3h

p < 0.01, logFC > 1 or p < 0.01, logFC < -1. Transcripts that showed significantly decreased expression in animals exposed to Camptothecin for 3 hours at 2C.