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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: Pseudomonas donghuensis HYS |
Transcripts that showed significantly decreased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to HYS. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00068216:FUR_vs_HYS_downregulated
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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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MicroRNAs that showed significantly increased 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_upregulated_miRNA_N2
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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 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) L3 larva comparing to in prg-1(wm161) L2 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_prg-1_L3_vs_L2_downregulated_adult
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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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Micro RNAs 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_miRNA
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microRNAs that showed significantly increased expression in male gonad comparing to in hermaphrodite gonad. |
DESeq2. miRNAs were considered significantly expressed between male and hermaphrodite if they had log2(fold change) > 1 and P-adj < 0.01. |
WBPaper00067242:male_vs_hermaphrodite-gonad_upregulated
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