Fig. 1

RNA-seq analysis of transcript levels in thapsigargin-stimulated and nutrient-starved murine enteroids. a Experimental design of samples submitted for RNA-seq. Intestinal organoid cultures were derived from three separate mice per condition. RNA was purified from organoids stimulated with either thapsigargin or nutrient-starved for 4 h and sent for RNA-seq. b Overview of the total number of genes analyzed (average over three replicates), including the adjusted total number of genes excluding those which had RPKM values >0. c, d Scatterplot analysis of the log10 changes in expression of the total (adjusted for RPKM values >0) number of genes in thapsigargin versus control enteroids (c) and nutrient starved versus control enteroids (d). e Violin scatter boxplot analysis of the genes induced and repressed more than 2.5 fold upon thapsigargin treatment and nutrient starvation. f Average fold change overall in the genes analyzed upon thapsigargin and nutrient starvation