Genome-wide identification of transcription factor ATOH1 target genes in adult small intestine and colon.

We generated three mRNA expression profiles by RNA-Seq of (i) wild-type crypts, (ii) Atoh1 knockout crypts, and (iii) purified ATOH1-positive cells. Overall design: We isolated Atoh1 knockout and littermate wild-type crypts from 6-8 week old Atoh1lox/lox;VilCreERT2 and Atoh1lox/WT;VilCreERT2 mice, respectively. In addition, ATOH1-positive cells were isolated by flow cytometry of 7AAD-negative (live), GFP-positive cells from either ileal or colonic crypts of Atoh1GFP/GFp mice (which express a functional ATOH1::GFP protein and are phenotypically normal).