Profiling the endothelial translatome in vivo using ‘AngioTag’ zebrafish (reanalysis)

We profiled the gene expression patterns of undisturbed endothelial cells in living animals using a novel ‘AngioTag’ zebrafish transgenic line that permits isolation of actively translating mRNAs from endothelial cells in their native environment. This transgenic line uses the endothelial cell-specific kdrl promoter to drive expression of an epitope tagged Rpl10a 60S ribosomal subunit protein, allowing for Translating Ribosome Affinity Purification (TRAP) of actively translating endothelial cell mRNAs. We also collected the whole embryo translatome using the TRAP protocol and a ubiquitously expressed tagged Rpl10a, and the endothelial transcritome by collecting the GFP+ endothelial cells that had the kdrl promoter driving GFP. Examination of 24hpf zebrafish whole embryo translatome, 24hpf zebrafish endothelial translatome, and 24hpf zebrafish endothelial transciptome mRNA levels. RNAseq analysis was redone using GRCz11 zebrafish reference genome and Ensembl version 99 models for protein-coding genes on the following GEO sample accessions: GSM3452116, GSM3452117, GSM3452118, GSM3452119, GSM3452120, GSM3452121, GSM3452122, GSM3452123, GSM3452124, GSM3452125, GSM3452126, GSM3452127, GSM3452128, GSM3452129, GSM3452130, GSM3452131, GSM3452132, GSM3452133. *************************************************************** The table below lists GEO accessions reused/reanalyzed for this study. ***************************************************************