RNA-seq profiles of Tp53, Prkar1a and Axin1 edited basal organoids from a mouse model of breast cancer

This study demonstrates the applicability of an in vivo CRISPR/Cas9 genome-wide screen in the BALB/c-Trp53+/– mouse model of breast cancer to identify novel tumor suppressor genes involved in mammary tumorigenesis. Preneoplastic mammary organoids were established from using sorted basal cells isolated from BALB/c-Trp53+/– mice. CRISPR/Cas9 screening was used to target Trp53, Axin1 and Prkar1a. To explore the potential molecular basis of the morphological differences, RNA-seq analysis was used to compare the Axin1/Trp53 and Prkar1a/Trp53-edited organoids and to organoids targeted by Trp53-only guides. Three biological replicates were prepared of Tp53, Tp53/Prkar1a and Tp53/Axin1 edited organoids. RNA-seq profiles of the 9 independent samples were sequenced on an Illumina NextSeq 500 to produce 75bp paired-end reads. Two sequencing runs were performed to increase sequencing depth for all the samples.