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Transcripts depleted in purified oocyte P bodies comparing to in the whole animal. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00065975:P-body_vs_WholeAnimal_depleted
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Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. |
CuffDiff, fold change > 2. |
WBPaper00065096:Day10_vs_Day1_upregulated
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Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. |
DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. |
WBPaper00054493:hpl-2(tm1489)_downregulated
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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 detected in germline isolated from day-1 adult hermaphrodite animals. |
All three experiments have CPM >= 1. |
WBPaper00067147:germline_expressed
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Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis. |
Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. |
WBPaper00040560:hpl-2_embryo_downregulated
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Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2 |
WBPaper00058725:sftb-1(cer6)_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 enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector. |
Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples. |
WBPaper00051039:germline_enriched
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Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing. |
DESeq2, fold change > 2,, p-value < 0.01 |
WBPaper00055334:DLC-1_interacting
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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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Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. |
Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. |
WBPaper00049377:MWCNT_downregulated
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Transcripts that showed significantly decreased expression after 24 hours of induction of human beta Amyloid at young adult stage |
A 2-fold change in expression level and a false discovery rate analog of p < 0.05. |
WBPaper00064130:Beta-Amyloid_24h_downregulated_mRNA
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Genes that exhibit a differential enrichment (p-value < 0.05 and a fold enrichment (log2fold)> 0.5) between the ADR-2 IPs from N2 and adr-2(ok735)worms. |
DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. |
WBPaper00055226:ADR-2_target_N2
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Transcripts that showed significantly increased expression in strain CER276 sftb1(cer39[Q552P, R643C,K718E]) comparing to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2 |
WBPaper00058725:sftb-1(cer39)_upregulated
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ncRNAs with significantly decreased expression in cep-1(gk138) than in N2 after UV irradiation, according to RNAseq. |
ncRNAs with more than 2 fold difference in expression are considered differentially expressed |
WBPaper00045380:cep-1(gk138)_downregulated_UV
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Transcripts that showed significantly increased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals. |
Limma Package. When generating the contrast matrix in limma: wildtype data was counted as wild-type and rpl-33 & rpl-5 data were both counted as RP null data. For this reason there is only one fold change value per gene as calculated by the difference between RP null RNA and wild-type RNA. |
WBPaper00056293:rpl-5(0)-rpl-33(0)_upregulated
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