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    Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma (2019)
    Springer Nature
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    Publication Date: 2019
    Description: 〈p〉Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long non-coding RNA (lncRNA) studies are limited. We report that plasma contains fragmented mRNAs and lncRNAs that are missed by standard small RNA-seq protocols due to lack of 5' phosphate or presence of 3' phosphate. These fragments were revealed using a modified protocol ("phospho-RNA-seq") incorporating RNA treatment with T4-polynucleotide kinase, which we compared with standard small RNA-seq for sequencing synthetic RNAs with varied 5' and 3' ends, as well as human plasma exRNA. Analyzing phospho-RNA-seq data using a custom, high-stringency bioinformatic pipeline, we identified mRNA/lncRNA transcriptome fingerprints in plasma, including tissue-specific gene sets. In a longitudinal study of hematopoietic stem cell transplant patients, bone marrow- and liver-enriched exRNA genes were tracked with bone marrow recovery and liver injury, respectively, providing proof-of-concept validation as a biomarker approach. By enabling access to an unexplored realm of mRNA and lncRNA fragments, phospho-RNA-seq opens up new possibilities for plasma transcriptomic biomarker development.〈/p〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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  • 2
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    Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉A modified RNA-seq method (Phospho-RNA-seq) revealed a new population of mRNA/lncRNA fragments in plasma, including ones that track with disease. This opens up new possibilities for disease detection via RNA profiling of plasma and other biofluids.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉Phospho-RNA-seq reveals a large population of mRNA and long non-coding RNA fragments in human plasma, which are missed by standard small RNA-seq protocols that depend on target RNAs having a 5' P and 3' OH.〈/p〉〈/li〉 〈li〉〈p〉Accurate detection of plasma mRNA and lncRNA fragments requires a stringent bioinformatic analysis pipeline to avoid false positive alignments to mRNA and lncRNA genes.〈/p〉〈/li〉 〈li〉〈p〉Phospho-RNA-seq identified ensembles of tissue-specific transcripts in plasma of hematopoietic stem cell transplant patients, which show co-expression patterns that vary dynamically and track with pathophysiological processes.〈/p〉〈/li〉 〈li〉〈p〉By enabling access to an unexplored space of extracellular mRNA and lncRNA fragments, phospho-RNA-seq opens up new possibilities for monitoring health and disease via transcriptome fragment profiling of plasma and potentially other biofluids.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
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