We analyzed the transcriptome of 45 organoid samples, corresponding to multiple clones and three differentiation time points for 4 families, including a father and a probands. Reads were aligned to the human hg19 reference genome with Tophat (Trapnell et al., 2010). Gene expression levels were estimated both as RPKM and counts using GencodeV7 gene annotation. RPKM values were estimated by using RSEQTools (Habegger et al., 2011). Counts were estimated by using BEDTools (Quinlan and Hall, 2010). After filtering out low expression genes, we inferred differentially expressed genes by edgeR (Robinson et al., 2010). Coexpressed gene modules were generated by WGCNA (Langfelder and Horvath, 2008) using log2(RPKM+1) as input, after filtering out low variance genes. DAVID (Dennis et al., 2003) and MSigDB v4.0 (Subramanian et al., 2005) were used for overrepresentation in Gene Ontologies and Canonical Pathways.
