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.

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.

WBPaper00057162:meg-3_meg-4_upregulated_sRNA

DESeq2 Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2

WBPaper00057162:meg-3_meg-4_downregulated_sRNA

DESeq2 Genes with small RNAs downregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2

WBPaper00056868:P.aeruginosa_downregulated_smallRNA

DESeq2, FDR < 0.05 Small RNAs (21-26nt) that showed significantly decreased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours.

WBPaper00056868:P.aeruginosa_upregulated_smallRNA

DESeq2, FDR < 0.05 Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours.

WBPaper00045090:RDE-12_dependent

N.A. Target genes whose small RNA levels are reduced more than 3-fold in the rde-12 mutants compared to N2 in the ERGO-1 and RDE-1 pathways. The minimal read cutoff is 20 in this analysis

WBPaper00053318:mir-71(n4115)_downregulated_mRNA

Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. Transcripts that showed significantly decreased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite.

WBPaper00053318:mir-71(n4115)_upregulated_miRNA

Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite.

WBPaper00053318:Aging_upregulated_miRNA_N2

Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. MicroRNAs that showed significantly increased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals.