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Transcripts that showed significantly decreased expression in skn-1gf(lax188) comparing to in N2 animals at L4 stage fed with OP50 and exposed to PA14 for 4 hours. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00067255:skn-1(lax188)_downregulated_PA
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Transcripts that showed significantly increased expression in eat-2(ad465);dve-1(RNAi) animals comparing to eat-2(ad465) animals injected with empty vector. |
fold change > 2, FDR < 0.01 |
WBPaper00067391:dve-1(RNAi)_upregulated_eat-2(ad465)
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Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage. |
DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. |
WBPaper00066110:tetraploid_vs_diploid_downregulated
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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 decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:eat-2(ad1116)_downregulated
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Single-cell RNA-Seq cell group 30_0 expressed in valve. |
scVI 0.6.0 |
WBPaper00065841:30_0
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Bacteria infection: Bacillus thuringiensis |
Transcripts that showed significantly decreased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304. |
N.A. |
WBPaper00064229:B.thuringiensis-Cry5Ba_downregulated
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Genes down-regulated after 24 hour exposure to colistin. |
Gene lists were created using a cutoff P-value of < 0.05, 2-fold change. |
WBPaper00045673:colistin_downregulated
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Transcripts that showed significantly decreased expression in hda-2(ok1479) comparing to in N2 animals. |
DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. |
WBPaper00062159:hda-2(ok1479)_downregulated
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Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP), comparing to in N2 animals. |
edgeR p-value < 0.01 and fold change > 4. |
WBPaper00061613:human-amyloid-beta_upregulated
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Transcripts that showed significantly decreased expression in ADL neurons of qui-1(db104) comparing to in N2 at day 1 adult stage. |
tximport 1.14.2 and DEseq2 1.26.0. Fold change > 2, FDR < 0.05. |
WBPaper00062520:qui-1(db104)_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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Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Rifampicin-Psora_downregulated
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Targets of endo-siRNA that showed significantly decreased expression in BFF40[meg-3(tm4259);meg-4(ax2026);mex-5::gfp::h2b::tbb-2] comparing to in SX1263[Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)] dissected gonad isolated from 1-day old adult hermaphrodites. |
DESeq2, fold change > 2, FDR < 0.01 |
WBPaper00057140:meg-3(tm4259)_meg-4(ax2026)_downregulated
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Transcripts that showed significantly decreased expression in mrps-5(RNAi) comparing to in control animals. |
Fold change > 4, p-value < 0.01 |
WBPaper00056330:mrps-5(RNAi)_downregulated
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Transcripts that showed significantly decreased expression in exos-8(RNAi) animals. |
fold change > 2, FDR < 0.05 |
WBPaper00068292:exos-8(RNAi)_downregulated
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Transcripts that showed significantly increased expression in animals with pan-neuronal expression of both human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP) and human alpha-Synuclein(A53T) (aex-3p-alpha-syn (A53T)), comparing to in N2 animals. |
edgeR p-value < 0.01 and fold change > 4. |
WBPaper00061613:human-amyloid-beta_alpha-Synuclein(A53T)_upregulated
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Transcripts that showed significantly decreased expression in diploid N2 animals after exposure to 5 uM doxorubicin for 72 hours at 15C from L1 to L4 larve stage. |
DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. |
WBPaper00066110:Doxorubicin_downregulated_diploid
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Transcripts that showed significantly decreased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa. |
DESeq2, FDR <0.05, fold change > 2. |
WBPaper00059664:srbc-48(ac23)_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Psora-Allantoin_downregulated
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Transcripts that showed significantly decreased expression in N2 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. |
edgeR (version 3.24.3), fold change > 4, FDR < 0.01. |
WBPaper00062456:doxycycline_downregulated_N2_transcript
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Transcripts that showed significantly decreased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms. |
DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) |
WBPaper00060764:swsn-1(os22ts)_downregulated
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Transcripts that showed significantly decreased expression in unc-30(ok613) animals at L4 larva stage after 4 hours of Pseudomonas aeruginosa infection, comparing to infected N2 animals. |
Genes exhibiting at least two-fold change were considered differentially expressed. |
WBPaper00061439:unc-30(ok613)_downregulated_P.aeruginosa-infection
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Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2. |
DESeq2, fold change > 2, p-value < 0.01. |
WBPaper00061203:sin-3(tm1276)_downregulated
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Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
DESeq2, fold change > 2, adjusted p-value < 0.01 |
WBPaper00058598:sin-3(tm1276)_upregulated
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Transcripts that showed significantly decreased expression in tdc-1(n3419);odIs77 comparing to in odIs77 control animals. |
EdgeR, FDR<0.01 |
WBPaper00060921:tdc-1(n3419)_downregulated
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Transcripts that showed lower expression in neurons isolated from male day 2 vs day 8. |
DESeq2 analysis was then employed for read normalization and differential expression analysis of the counted reads. PCA analysiswas performed along with the DESeq2 package. Genes with a log2(fold-change) > 1 and p-adjusted < 0.05 were considered differentially expressed in subsequent analysis. |
WBPaper00066831:male-neuron_aging_upregulated
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Transcripts that showed significantly decreased expression in VC1743[mett-10(ok2204)] comparing to in N2 when animals grow on standard (OP50) plates. |
DESeq2, p-value < 0.05, fold change > 2. |
WBPaper00061357:mett-10(ok2204)_downregulated_OP50
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Transcripts that showed significantly decreased expression in mbl-1(tm1563) comparing to in N2 animals. |
Differential expression analysis was performed using the EdgeR package after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples. |
WBPaper00062167:mbl-1(tm1563)_downregulated
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