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miRNAs that showed increased expression after exposure to graphene oxide (GO) |
The dysregulated expression of miRNAs in GO-exposed nematodes was analyzed by DESeq (an R package, a powerful tool to estimate the variance and test for differential expression). The data were extracted as up- or down-regulated miRNAs according to a cutoff of 2 fold change, and were presented in the scatter diagram after normalization. |
WBPaper00045209:graphene-oxide_upregulated
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Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure. |
Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours. |
DESeq2, FDR < 0.05 |
WBPaper00056868:P.aeruginosa_upregulated_smallRNA
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Transcripts that showed significantly decreased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066485:ogt-1(ok1474)_downregulated_neuron
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Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in coelomocyte. |
Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. |
WBPaper00066447:Day8_vs_Day1_upregulated_coelomocyte
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Hypoxia: 0.5% oxygen 2 hours. |
Transcripts that showed significantly increased expression after hypoxia in an egl-9 / hif-1 independent manner. |
DESeq2 p-value <0.05, expression of hypoxia vs. normxia >= 2, expression in egl09(sa307) vs N2 < 2, expression of egl-9(sa307); hif-1(ia04) vs N2 <= 2. |
WBPaper00055344:hypoxia_regulated_HIF-1_independent
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MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-5(ram2)_downregulated_miRNA
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Micro RNAs that showed significantly decreased expression in hrpk-1(tm5522) comparing to in N2 at L4 larva stage. |
DESeq, fold change > 2, p-value <= 0.05. |
WBPaper00058673:hrpk-1(tm5522)_downregulated_miRNA_L4
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miRNA with increased expression in N2 1-day post L4 adult hermaphrodite comparing to in N2 L4 larva. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_N2_adult_vs_L4_upregulated_adult
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miRNA with decreased expression in N2 L1 larva comparing to in N2 embryo. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_N2_L1_vs_embryo_downregulated_adult
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MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-1(gk214)_downregulated_miRNA
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MicroRNAs that showed significantly decreased expression in alg-2(ok304), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-2(ok304)_downregulated_miRNA
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MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-2(ok304)_upregulated_miRNA
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_adult
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_embryo
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MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_L1
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_L2
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_L3
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_L4
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miRNA with decreased expression in prg-1(wm161) L1 larva comparing to in prg-1(wm161) embryo. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_L1_vs_embryo_downregulated_adult
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MicroRNAs that showed significantly increased expression in alg-5(ram2), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-5(ram2)_upregulated_miRNA
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Fasting for 48 hours, from 3 days post L4 to 5 days post L4. |
MicroRNAs that showed significantly increased expression after 48 hours of fasting |
p < 0.0002, Fishers exact test. |
WBPaper00051247:fasting_upregulated
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MicroRNAs that showed significantly increased 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)_upregulated_miRNA
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Bacteria infection: Pseudomonas aeruginosa PA14 |
miRNAs up regulated by Pseudomonas aeruginosa infection. |
N.A. |
WBPaper00046303:P.aeruginosa_upregulated_miRNA
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MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-1(gk214)_upregulated_miRNA
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space radition and microgravity |
Micro RNAs that showed increased expression in space flight N2 samples comparing to in ground control, affected by space radition and microgravity. |
Differentially expressed miRNAs (>1.5-fold change and <0.67) and mRNAs (>2-fold change and <0.5) were identified through fold-change filtering. |
WBPaper00048474:SpaceRadiation-Microgravity_upregulated_N2
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