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.

WBPaper00060014:set-2(tm1630)_upregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.

WBPaper00060014:set-2(zr2012)_downregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly decreased expression in set-2(zr2012) animals at embryo stage, comparing to in N2 animals.

WBPaper00060014:set-2(zr2012)_upregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly increased expression in set-2(zr2012) animals at embryo stage, comparing to in N2 animals.

WBPaper00060014:set-2(tm1630)_downregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.

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.