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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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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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miRNA that showed increased expression after 20mM nicotine treatment |
Statistical analysis was based on t-test for independent samples via SPSS. The results were further narrowed based on two criteria. Only the genes whose expression changed with a P < 0.05 and a fold change > 0.5, when compared to control, were considered as differentially expressed. Fold change was calculated as 2**(DeltaCt(treatment)-DeltaCt(control))-1. DeltaCt = Ct(miRNA)-Ct(aveMRNA). |
WBPaper00042480:20mM_nicotine_upregulated
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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 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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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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Heat Shock: 35C 4 hours at L4 larva stage. |
Micro RNAs that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours |
DESeq2 |
WBPaper00057154:HeatShock_downregulated_miRNA
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MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood mir-71(n4115) 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_miRNA_mir-71(n4115)
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MicroRNAs 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_miRNA_N2
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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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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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MicroRNAs that showed significantly decreased expression after animals were exposed to 1 mg per liter multi-walled carbon nanotubes (MWCNTs) from L1 larva to young adult. |
DESeq, cut-off of 2-fold change. |
WBPaper00045019:MWCNT_downregulated
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miRNAs that showed decreased 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_downregulated
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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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miRNAs in F2 generation up regulated by exposure to 20uM and 20mM nicotine during F0 generation. |
Statistical analysis was based on t-test for independent samples via SPSS to compare each of the nicotine treatments with control (i.e. low vs. control and high vs. control). Welch test correction was performed to account for unequal variance in each of the compared groups (control and treatment). In addition, to increase the statistical stringency, miRNAs differential expression was deemed significant only if it fulfilled two criteria: p value , 0.05 and expression changed by at least 50% relative to control. |
WBPaper00049006:nicotine_upregulated_F2
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