The BAF complex does not mediate GLI repression (RNA-Seq)

Purpose: This study seeks to determine whether Smarcc1 co-regulates Hedgehog (HH) target genes in the limb. Methods: To determine if Smarcc1 is required to regulate HH targets, we used genomic approaches to identify Smarcc1-regulated genes within the forelimb. We performed bulk RNA-seq on individually genotyped forelimb-bud pairs at E11.5 (39-40s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (2 replicates) embryos. From this experiment we identified 928 differentially expressed genes (FDR<0.05). Results: We find that while certain HH target genes are co-regulated by SMARCC1, the majority of HH target genes do not require Smarcc1. Bulk RNA-seq on individual E11.5 (39-40s) forelimb bud pairs from control (2 replicates) and PrxCre/+;Smarcc1c/c (2 replicates) embryos.