The in vivo endothelial cell translatome is highly heterogeneous across vascular beds (EC-TRAP RNAseq)

The interspersed anatomic distribution of endothelial cells (ECs) and their dependence on microenvironmental cues have been major challenges in studying EC function and response to (patho)physiological stimuli in vivo. Combining EC-specific translating ribosome affinity purification (EC-TRAP) with RNA sequencing provides an accurate in vivo snapshot of tissue-specific EC expression profiles, and maintains a high degree of sensitivity to detect low abundant transcripts while limiting changes in gene expression profiles due to enzymatic tissue dissociation required to generate single cell suspensions for FACS sorting or single cell analysis. In addition to demonstrating EC heterogeneity under physiologic conditions, the in vivo host response to lipopolysaccharide (LPS) revealed the induction of expression programs associated with a native defense response, with marked differences across vascular beds. Total tissue lysate and EC-TRAP RNASeq data of brain, heart, kidney, liver and lung from 10 week old Rpl22-floxed, Tek-Cre males under physiologic conditions or 4 hours after LPS treatment (n=3); total lysate and EC-TRAP RNASeq data of brain, kidney and liver after enzymatic tissue dissociation (n=3); RNASeq data from RBC-lysed whole blood before and after TRAP (n=2); RNASeq data (total lysate and EC-TRAP) from brain, heart, kidney and liver from Rpl22-floxed, Tek-Cre male after bone marrow transplantation with Cre-negative donor (n=1); RNASeq data from pooled platelets of Rpl22-floxed, Pf4-Cre before and after TRAP (n=1); total tissue lysate and TRAP data brain, heart, kidney, liver and lung from 10 week old Rpl22-floxed, EIIa-Cre males (n=3).