RNA-Seq of rRNA depleted circulating endothelial progenitor cells (cEPCs) in trisomy 21 and euploid samples

Massive-scale RNA-seq on rRNA-depleted samples allowed us to survey in a specific cell type, affected in Down syndrome, the complete set of coding and non-coding RNA species - emerging as novel contributors to pathogenic mechanisms - to an unprecedented level of resolution and sensitivity. In particular, we demonstrated the deregulation of crucial gene pathways by quantitatively measuring the expression of known RefSeq genes. Moreover, we identified novel regions of active transcription falling outside already annotated loci, and investigated also the expression of non-polyadenilated long, as well as short, non coding RNAs. In addition, we found novel splice isoforms for a large subset of genes, and novel extended UTRs, both 5' and 3', for known genes - possibly representing novel miRNA targets or regulatory sites for gene transcription, respectively. 2 RNA samples examined: 1 euploid control and 1 trisomic sample.