2016-06-03T16:37:08Z (GMT) by Carl S. Thummel William E. Barry
dHNF4-DNA bound complexes were immunoprecipitated using polyclonal antibody against endogenous dHNF4 protein. Barcoded libraries for dHNF4-IP and input control samples were generated by the University of Utah High Throughput Genomics core facility and sequenced in a single lane Illumina HiSeq 5-cycle single-read sequencing. Data analysis was performed by the Bioinformatics Core at the University of Utah School of Medicine using USeq and Model-based Analysis for ChIP-seq (MACS2) run with a peak shift of 100 bp. Enrichment peaks were identified with an FDR cutoff of 1% and nearest neighboring genes were compiled using USeq FindNeighboringGenes and UCSC dm3 EnsGenes gene tables. Nearest neighbor genes were compared to our RNA-seq dataset to identify neighbors that are also misexpressed in dHNF4 mutants, highlighting these as direct targets of dHNF4.