Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Deep-sequencing of endogenous microRNAs from human endothelial cells exposed to hypoxia and normoxia

ABSTRACT: Human Umbelical Vein Endothelial Cells (HUVEC) were cultured in vitro and exposed to 1% oxygen or normoxia for 24 hours. Then, small RNA libraries were prepared and sequenced using sequencing-by-ligation technique (Solid3 Plus Sequencer platform). Alignment versus miRBase v14.0 identified >400 different microRNA/microRNA* species expressed in HUVEC. A complex repertoire of isomiR was also observed. For novel miRNA discovery, reads were mapped against the human genome. We identified 511 candidate new microRNAs and we validated 18 of them with independent techniques. 4 samples: 2 independent HUVEC populations were analyzed, each both normoxic and hypoxic

ORGANISM(S): Homo sapiens

SUBMITTER: Fabio Martelli

PROVIDER: E-GEOD-26497 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs.

Voellenkle Christine C Rooij Jeroen van Jv Guffanti Alessandro A Brini Elena E Fasanaro Pasquale P Isaia Eleonora E Croft Larry L Croft Larry L David Matei M Capogrossi Maurizio C MC Moles Anna A Felsani Armando A Martelli Fabio F

RNA (New York, N.Y.) 20120126 3

In order to understand the role of microRNAs (miRNAs) in vascular physiopathology, we took advantage of deep-sequencing techniques to accurately and comprehensively profile the entire miRNA population expressed by endothelial cells exposed to hypoxia. SOLiD sequencing of small RNAs derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O₂ or normoxia for 24 h yielded more than 22 million reads per library. A customized bioinformatic pipeline identified more than 400 annotated ...[more]

PMID: 22282338

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Project description:Clonorchis sinensis is a zoonotic parasite causing clonorchiasis associated with human diseases such as biliary calculi, cholecystitis, liver cirrhosis, and is classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules essential for the complex life cycle of parasites and involved in parasitic infections. To identify and characterize miRNAs expressed in adult C. sinensis residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing, bioinformatic predictions with stem-loop real-time PCR analysis. Here we report the use of this approach to identify and clone 6 new and 62,512 conserved C. sinensis miRNAs which belong to 284 families. There is strong bias on families, family members and sequence nucleotides in C. sinensis. Uracil is the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and the end of conserved miRNAs. There is no significant M-bM-^@M-^\seed regionM-bM-^@M-^] at the first and ninth positions commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of C. sinensis are still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There are two miRNA strategies in C. sinensis for its parasitic life: keeping a large category of miRNA families of different animals and keeping a stringent conserved seed region with high active innovation in other place of miRNA mainly in the middle and the end, which are perfect for the parasite to perform its complex life style and for host changes. The present study represents the first large scale characterization of C. sinensis miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as the miRNA studies of other related species such as Opisthorchis felineus and O. viverrini of human and animal health significance. Analysis of miRNA profile in parasite of C. sinensis

Dataset Information

Deep-sequencing of endogenous microRNAs from human endothelial cells exposed to hypoxia and normoxia

Publications

Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs.

Similar Datasets

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