- WBPaper00065750:rumen-EVs_downrgulated
N.A.
Top 5 transcripts that showed significantly decreased expression after L4 animals were exposed to rumen-derived extracellular vesicles for 24 hours.
- WBPaper00065750:rumen-EVs_uprgulated
N.A.
Top 5 transcripts that showed significantly increased expression after L4 animals were exposed to rumen-derived extracellular vesicles for 24 hours.
- WBPaper00049489:AMsh-glia_enriched
Two different statistical methods were used for differential gene expression analysis, DESeq and voom. For DEseq analysis, DESeq2 was applied to normalize count matrix and to perform differential gene expression on the counts using negative binomial distribution; for voom analysis, edgeR was applied to normalize count matrix, and voom was applied for gene differentiation analysis. Significant genes from both analyses were combined. To identify transcripts enriched in AMsh glia compared to other cells (control AMsh versus control non-AMsh), authors used a fold change of 3.5 and an adjusted p value threshold of <0.05.
Genes enriched in AMsh glia.
- WBPaper00028360:Phospho-Sulfo-Modified_proteins
The protein identification was performed by PMF analysis with the spectra in the positive ion mode. Database searches against all entries of Refseq Release 13 were carried out using Biotools 2.2 (Bruker Daltonics) and MASCOT search engine (Matrix Science, London, UK). The search parameters allowed carbamidomethylation of Cys, partial oxidation of Met, 150 ppm for mass tolerance, and one missed cleavage per peptide. The protein identification results were accepted in consideration of the MASCOT score. Furthermore, the reliability of the results was confirmed by the additional information of the spectrum observed in the negative ion mode.
Phosphorylation and sulfonation peptides were detected by Mass Spectrometry using the positive and negative ion modes with mono-ammonium phosphate as the matrix additive.
- WBPaper00056293:rpl-5(0)-rpl-33(0)_upregulated
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.
Transcripts that showed significantly increased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals.
- WBPaper00056293:rpl-5(0)-rpl-33(0)_downregulated
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.
Transcripts that showed significantly decreased expression in rpl-5(cc5998) vs wild type (PD1074) and rpl-33(cc2558) vs wild type (PD1074) animals.
- WBPaper00005943:adult_specific
Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified.
Life stage specific marker proteins according to proteomic analysis. Adult specific.
- WBPaper00005943:L4-adult_specific
Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified.
Life stage specific marker proteins according to proteomic analysis. L4 and adult specific.
- WBPaper00005943:L1_specific
Database searches (MSDB, SWISS-PROT, and Wormpep databases) were performed using the Mascot software 1.8 (Matrix Science, London, UK) with carboxamidomethylation of cysteins set as fixed modifications and methionine oxidations set as variable modifications. Positive identification was achieved only when the quality criteria, 50 - 70 ppm mass accuracy and 1 or 2 miscleavage sites were met at significant probability score (usually above 100) and nearly all signals of the spectrum were assigned to the protein or mixture of proteins identified.
Life stage specific marker proteins according to proteomic analysis. L1 specific.