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Bacteria: E.faecalis strain OG1RF |
Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. |
Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. |
WBPaper00059754:E.faecalis_OG1RF_upregulated
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Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rifampicin-Allantoin_upregulated
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Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
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Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage. |
EdgeR, fold change > 2, FDR < 0.001. |
WBPaper00056290:hsp-6(mg585)_downregulated
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Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. |
DESeq2 version 1.22.2, p < 0.05 |
WBPaper00064716:paraquat_downregulated
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Transcripts that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals. |
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. |
WBPaper00053318:Aging_downregulated_mRNA_N2
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Transcripts that showed significantly decreased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite. |
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. |
WBPaper00053318:mir-71(n4115)_downregulated_mRNA
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Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. |
Log2 Fold change > 2 or <-1, p-value < 0.05. |
WBPaper00053599:female_vs_male_downregulated
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Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 25C, comparing to in N2 animals. |
CuffDiff, fold change > 2. |
WBPaper00065096:npr-8(ok1439)_upregulated_Day10_25C
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Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. |
Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. |
WBPaper00061479:hda-1(ne4752)_upregulated
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Transcripts that showed significantly increased expression in prg-1(tm872) in gonads dissected from 1-day old adult animals. |
Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. |
WBPaper00061479:prg-1(tm872)_upregulated
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Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066594:ilc-17.1(syb5296)_upregulated
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Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals. |
DESeq2 v. 1.22.2, adjusted p-value <= 0.05. |
WBPaper00059605:mut-16(pk710)_upregulated
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Transcripts that showed significantly increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage. |
Fold change > 2, FDR < 0.05. |
WBPaper00066608:npr-15(tm12539)_upregulated
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Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:eat-2(ad1116)_downregulated
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Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. |
Student's t-test, fold change > 2, p-value < 0.05. |
WBPaper00055386:daf-2(e1370)_upregulated
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Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin. |
N.A. |
WBPaper00055862:antimycin_damt-1(gk961032)_regulated
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Proteins identified in extracellular vesicle. |
N.A. |
WBPaper00062669:extracellular-vesicle_protein
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Transcripts that showed significantly decreased expression in nhr-114(gk849) comparing to wild type animals at L4 larva. |
DESeq2 1.26.0, fold change > 2, FDR < 0.05. |
WBPaper00064539:nhr-114(gk849)_downregulated
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Transcripts that showed significantly increased expression in sma-2(rax5) comparing to in N2 at 1-day post-L4 adult hermaphrodite |
HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05. |
WBPaper00053184:sma-2(rax5)_upregulated
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Transcripts that showed significantly increased expression in sma-4(rax3) comparing to in N2 at 1-day post-L4 adult hermaphrodite |
HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05. |
WBPaper00053184:sma-4(rax3)_upregulated
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Temprature shift to 28C for 24 hours. |
Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 24 hours. |
Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. |
WBPaper00061341:28C_24h_upregulated
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Temprature shift to 28C for 48 hours. |
Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours. |
Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. |
WBPaper00061341:28C_48h_upregulated
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Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
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Transcripts that showed significantly increased expression in pals-17(syb3980) comparing to in N2 animals at young adult stage. |
Differential expression analyses were performed using limma-voom in Galaxy, adj p <= 0.05, logFC > 2 |
WBPaper00065984:pals-17(syb3980)_upregulated
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Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. |
Transcripts that showed significantly increased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50. |
Cuffcompare and Cuffdiff |
WBPaper00056090:E.faecalis_upregulated_N2
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Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite npr-8(ok1439) animals grown at 25C, comparing to in N2 animals. |
CuffDiff, fold change > 2. |
WBPaper00065096:npr-8(ok1439)_upregulated_Day1_25C
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Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals. |
CuffDiff, fold change > 2. |
WBPaper00065096:npr-8(ok1439)_upregulated_Day10_20C
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siRNAs that showed significantly lower expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine). |
DESeq2 v1.13.8, fold change > 2, FDR < 0.01. |
WBPaper00056161:male_enriched_siRNA
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