RNA sequencing of 4N intestinal and non-intestinal C. elegans cells in L1

Endomitosis is a non-canonical cell cycle in which cells undergo all four phases of a canonical cell cycle (G1, S, G2 and M), but do not initiate or complete cytokinesis during M phase. To identify the transcriptional differences between endomitosis and canonical cell cycles in C. elegans, we isolated cells from L1 larvae of a strain expressing intestinal-specific mCherry (elt-2p::mCherry-PH-P2A-H2B-mCherry) grown for 6 hours at 20ºC. We sorted intestinal and non-intestinal cells both with a 4N DNA content by FACS based on the mCherry expression and the Hoechst-34580 profile. We performed RNA-seq in intestinal (3 replicates) and non-intestinal cells (3 replicates) and differential gene expression analysis to identify the genes that are upregulated or downregulated in intestinal endomitosis compared to canonical cell cycles. Overall design: mRNA profiles of intestinal (3 biological replicates) and non-intestinal cells (3 biological replicates) generated from pools of 500 cells with an adapted CEL-seq protocol and paired-end sequencingon an Illumina NextSeq500 platform.