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Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. |
DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. |
WBPaper00048971:daf-16(mgDf50)_downregulated_L1
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Genes expressed in N2. |
Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. |
WBPaper00025141:N2_Expressed_Genes
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EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the third UVC dose (51h), which is also 3 h after being placed on food. |
Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -3h timepoint (3 h after the third UVC dose (51h), which is also 3 h after being placed on food). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:EtBr-exposed_vs_UVC-exposed_51h
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24 hours of AgNPs exposure. |
Genes downregulated more than 2 fold after 24 hours of AgNPs exposure. |
Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL). |
WBPaper00034661:AgNPs_downregulated
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Genes depleted in muscle cells (24hr muscle dataset). Dissociated myo-3::GFP embryos were cultured for 24 hours before FACS sorting. |
A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. |
WBPaper00031003:24hr_muscle_depleted
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Total muscle depleted genes (complete list of non-overlapping genes from the 0hr and 24hr muscle depleted datasets). |
A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. |
WBPaper00031003:total_muscle_depleted
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control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h). |
Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -1h timepoint. |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:control_vs_EtBr-exposed_48h
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control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h). |
Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:control_vs_UVC-EtBr-exposed_48h
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UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the third UVC dose (48h). |
Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:UVC-EtBr-exposed_vs_UVC-exposed_48h
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Genes expressed in embryonic motor neurons (identified by unc-4::GFP expressing cells). |
Genes called Present by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations. |
WBPaper00025141:unc-4::GFP_Expressed_Genes
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Genes down regulated in the absence of TDP-1, when the threshold was set at a fold change (FC) of 1.2. |
The management and statistical analysis of the microarray data were performed using the Partek Genomic Suite (Partek, Missouri) and Spotfire DecisionSite software (TIBCO, California). |
WBPaper00040603:tdp-1(lf)_down_vs_N2_FC_1.2
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control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the third UVC dose (51h), which is also 3 h after being placed on food. |
Genes differentially expressed in control vsafter UVC exposure without EtBr treatment, at the 3h timepoint (3 h after the third UVC dose (51h), which is also 3 h after being placed on food). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:control_vs_UVC-exposed_51h
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4 hours of starvation. |
Genes with significantly increased expression in N2 animals after 4 hours of starvation. |
Differentially expressed genes were determined by ANOVA analysis using the Partek software package. |
WBPaper00047070:N2_starvation_upregulated
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Starvation 2-4 hours at L1 larva stage since hatching. |
Genes that showed significantly changed expression by starvation for 2-4 hours after hatch, by comparing N2 starved and N2 fed animals at L1 larva. |
Normalized log2 GCRMA values were used to assess significance of expression changes with the LIMMA/GCRMA empirical Bayes test. A threshold for significance at a q-value (FDR) of less than 0.05 was used to determine if a gene is differentially expressed. |
WBPaper00053236:Starvation_regulated_N2
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EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the third UVC dose (48h). |
Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:EtBr-exposed_vs_UVC-exposed_48h
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Larval Pan-neural Enriched Genes. |
A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. |
WBPaper00030839:Larval_Pan_Neuronal
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WT-Pico Pan-neural Enriched Genes, with genes found multiple times in a single dataset removed (without dups). |
To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. |
WBPaper00031532:Larva_Pan_Neuronal_Enriched
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Starvation 2-4 hours at L1 larva stage since hatching. |
Genes that showed significantly changed expression by starvation for 2-4 hours after hatch, by comparing GR1307[daf-16(mgDf50)] starved and GR1307[daf-16(mgDf50)] fed animals at L1 larva. |
Normalized log2 GCRMA values were used to assess significance of expression changes with the LIMMA/GCRMA empirical Bayes test. A threshold for significance at a q-value (FDR) of less than 0.05 was used to determine if a gene is differentially expressed. |
WBPaper00053236:Starvation_regulated_GR1307
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UV irradiation: 10 mJ per square cm. |
Genes with significantly decreased expression in xpa-1(ok698) animals after treated with 10mJ per square cm UV and harvested 6 hours later. |
Differentially expressed genes were determined by ANOVA analysis using the Partek software package. |
WBPaper00047070:xpa-1_UV_downregulated
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control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the first UVC dose (3h). |
Genes differentially expressed in control vsafter UVC exposure without EtBr treatment, at the -45h timepoint (3 hours after the first UVC dose). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:control_vs_UVC-exposed_3h
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EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at 3 h after the first UVC dose (3h). |
Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -45h timepoint (3 hours after the first UVC dose). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:EtBr-exposed_vs_UVC-exposed_3h
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Genes depleted in muscle cells (0hr muscle dataset). Dissociated myo-3::GFP embryos were cultured for 0 hours before FACS sorting. |
A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. |
WBPaper00031003:0hr_muscle_depleted
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Transcripts that showed significantly increased expression after exposure of to 10 mg per liter of SiNPs for 24 h. |
Fold change and Welcht-test performed between probes per gene and were applied to selectdifferentially expressed genes (DEGs): the fold change threshold was 2-fold and the significance level was p < 0.05. |
WBPaper00057098:SiO2-nanoparticles_upregulated
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Larval A-class motor neuron enriched genes. |
A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. |
WBPaper00030839:Larval_A_Class
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Transcripts of noncoding genes that showed significantly decreased expression in muscle. |
DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. |
WBPaper00062325:muscle_depleted_noncoding-RNA
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