Transcriptomic responses were assessed 6 and 12 h after exposure to the respective bacteria. At the respective time points, worms were washed off the assay plates with PBS containing 0.3% Tween20, and subsequently centrifuged. The worm pellet was resuspended in 800 μl TRIzol (Life Technologies) reagent and worms were broken up prior to RNA extraction by treating the worm suspension five times with a freeze-and-thaw cycle using liquid nitrogen and a thermo block at 45°C. RNA was extracted using a NucleoSpin miRNA extraction kit (Macherey-Nagel), treated with DNAse, and stored at -80°C. RNA libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on an Illumina HiSeq 2000 sequencing machine with paired-end strategy at read length of 100 nucleotides. The raw data is available from the GEO database [34, 35] under GSE110913.

RNA-Seq reads were firstly trimmed for adaptor sequence, masked for low quality sequence via Trimmomatic [36] and then mapped to the C. elegans genome (WormBase web site, http://www.wormbase.org, release WS235) by STAR 2.5.3a [37] under default setting. Transcription abundance (read counts per gene) was extracted via HTSeq [38]. Differential expression analysis was performed by aFold from ABSSeq [39]. We only considered genes with a significant change between conditions (clec-4 mutant vs. N2; adjusted p-value < 0.01). The log2 transformed fold-changes were taken as input for k-means cluster analysis using cluster 3.0 [40]. A heatmap was generated by TreeView version 1.1.4r3 [41].

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