NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]. NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

We analyzed binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity using nextPBM, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative factors (C/EBPa) Overall design: Genome-wide binding of 3 monocyte/macrophage lineage-determining TFs (PU.1, C/EBPa, and IRF8) and locations of enhancer-related histone marks (H3K4me1 and H3K27ac) in THP-1 cells. Each experiment was performed across 2 biological replicates. Biological replicates were analyzed separately up until the peak filtering step where the Irreproducible Discovery Rate (IDR) was used as a cross-replicate reproducibility filter. Results were then used in the design of a custom array for the nextPBM protein-binding experiments