WBPaper00061651:DA_enriched

Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. Transcripts enriched in DA according to single cell RNAseq.

WBPaper00065560:E.coli-HB101_downregulated_F3

Differentially expressed genes were extracted using DESeq, version 1.10.1. Assembly: PRJNA13758.WBPS13 Transcripts downregulated in F3 generation of transgenic C. elegans expressing human alpha-syn in DA neurons fed HB101 0E. coli vs. OP50.

WBPaper00065560:E.coli-HB101_upregulated_P0

Differentially expressed genes were extracted using DESeq, version 1.10.1. Assembly: PRJNA13758.WBPS13 Transcripts upregulated in P0 generation of transgenic C. elegans expressing human alpha-syn in DA neurons fed HB101 0E. coli vs. OP50.

WBPaper00065560:E.coli-HB101_upregulated_F3

Differentially expressed genes were extracted using DESeq, version 1.10.1. Assembly: PRJNA13758.WBPS13 Transcripts upregulated in F3 generation of transgenic C. elegans expressing human alpha-syn in DA neurons fed HB101 0E. coli vs. OP50.

WBPaper00065560:E.coli-HB101_downregulated_P0

Differentially expressed genes were extracted using DESeq, version 1.10.1. Assembly: PRJNA13758.WBPS13 Transcripts downregulated in P0 generation of transgenic C. elegans expressing human alpha-syn in DA neurons fed HB101 0E. coli vs. OP50.

WBPaper00050514:CEBP-1_interacting

CHIP-seq. Authors conducted peak calling using a CLC Genomics Workbench 6.0. Transcripts physically interacting with CEBP-1 protein, according to CHIP-Seq analysis by immunoprecipitating FLAG-CEBP-1-associated withh DA fragments using anti-FLAG antibody.

WBPaper00053388:dauer_regulated_Cluster1

Benjamini Hochberg corrected q-value < 0.01. Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. The expression levels of Cluster 1 gradually decreased into dauer.

WBPaper00053388:dauer_regulated_Cluster6

Benjamini Hochberg corrected q-value < 0.01. Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 6 genes increased expression in L4.

WBPaper00059328:mrps-5(RNAi)_upregulated_mRNA

Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. Transcripts that showed significantly increased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector.

WBPaper00059328:mrps-5(RNAi)_downregulated_protein

Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. Proteins that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector.