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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell.

Xing Tang, Mei Hou, Yang Ding

    BMC Genomics
    |February 26, 2014
    PubMed
    Summary
    This summary is machine-generated.

    Researchers identified 300 human embryonic stem cell long intergenic non-coding RNAs (lincRNAs), with 78 showing biased expression involved in early development. A web portal offers access to these crucial regulators for further study.

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    Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells
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    Area of Science:

    • Stem cell biology
    • Genomics
    • Non-coding RNA research

    Background:

    • Long intergenic non-coding RNAs (lincRNAs) play roles in pluripotency and differentiation, but their global impact on cell fate is unclear.
    • Systematic profiling and annotation of embryonic stem cell lincRNAs are needed to understand their functions.

    Purpose of the Study:

    • To systematically identify and annotate long intergenic non-coding RNAs (lincRNAs) in human embryonic stem cells (hESCs).
    • To investigate the expression patterns and functional involvement of identified hESC lincRNAs.
    • To create a publicly accessible resource for hESC lincRNA data.

    Main Methods:

    • Utilized multiple RNA-sequencing (RNA-Seq) datasets for systematic identification.
    • Performed functional enrichment analysis and comparative genomics.
    • Developed an interactive online portal for data access and analysis.

    Main Results:

    • Identified 300 human embryonic stem cell lincRNAs (hES lincRNAs).
    • Found 78 (one-fourth) hES lincRNAs were biasedly expressed in hESCs and involved in early development.
    • Approximately half of the identified lincRNAs were conserved in mouse.
    • Launched a web portal (http://scbrowse.cbi.pku.edu.cn) with navigation and query tools.

    Conclusions:

    • Successfully characterized and annotated 300 hES lincRNAs by integrating RNA-Seq data.
    • The developed web portal provides a valuable resource for studying hESC lincRNAs.
    • This work offers the first global profiling and annotation of hESC lincRNAs, aiding researchers in the field.