Bulk RNA-seq analysis of Delta-like 4 (Dll4) knockdown in LPS- or TNF-α-stimulated THP-1 cells

Here, we investigated the contribution of delta-like 4 (Dll4)-Notch signaling in monocyte-mediated inflammation. To investigate the biological functions and molecular mechanisms of monocyte Dll4, bulk RNA sequencing (RNA-seq) was performed in THP-1 cells transfected with Dll4 siRNA or control siRNA for 24 hours in the presence of LPS or TNF-α stimulation.

Four experimental groups were analyzed: control siRNA + LPS, Dll4 siRNA + LPS, control siRNA + TNF-α, and Dll4 siRNA + TNF-α. Each group included five biological replicates (n=5 per group). The RNA-seq analysis was designed as a discovery experiment powered to detect moderate-to-large expression differences.