Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Valerio Costa

PROVIDER: E-GEOD-27443 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.

Costa Valerio V Angelini Claudia C D'Apice Luciana L Mutarelli Margherita M Casamassimi Amelia A Sommese Linda L Gallo Maria Assunta MA Aprile Marianna M Esposito Roberta R Leone Luigi L Donizetti Aldo A Crispi Stefania S Rienzo Monica M Sarubbi Berardo B Calabrò Raffaele R Picardi Marco M Salvatore Paola P Infante Teresa T De Berardinis Piergiuseppe P Napoli Claudio C Ciccodicola Alfredo A

PloS one 20110420 4

Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of published works has still described the whole transcriptional landscape of Down syndrome. Although the recent advances in high ...[more]

PMID: 21533138

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Project description:How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment, the nature of which is far from being clear. In the case of the lymphatic system, venous endothelial cells are thought to give rise to lymphatic vessels, through a process of trans-differentiation. Upon expression of a set of transcription factors, venous cells acquire a lymphatic fate, and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells (LECs) do arise in the Cardinal Vein (CV), they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic-specific transgenic zebrafish, in combination with endothelial photoconvertible reporters, and long-term live imaging, we demonstrate that these multipotent angioblasts can generate not only lymphatic, but also arterious, and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b, which acts as a lymphatic inductive signal, promoting the angioblast-to-lymphatic transition. Moreover, Wnt5b induced lymphatic specification in human embryonic stem cells- derived vascular progenitors, suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation, whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium, and provide the first characterization of their inductive niche. More broadly, our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations, analogous to the hematopoietic niche in the aortic floor. Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tg(fli1:gal4;uasKaede) embryos at 24 hpf, 6 embryos per group were used for FACS isolation of Kaede photconverted (red) ECs.

Dataset Information

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

Publications

Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.

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