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Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond

View ORCID ProfileLu Li, Jin Feng Li, Dan Dan Cao, Vassilios Papadopoulos, Wai Yee Chan
doi: https://doi.org/10.1101/784819
Lu Li
1CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
2Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
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  • For correspondence: lli172@usc.edu chanwy@cuhk.edu.hk
Jin Feng Li
3Department of Computer Science and Engineering, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
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Dan Dan Cao
1CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
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Vassilios Papadopoulos
2Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
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Wai Yee Chan
1CUHK-CAS GIBH Joint Research Laboratory on Stem Cell and Regenerative Medicine, School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
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  • For correspondence: lli172@usc.edu chanwy@cuhk.edu.hk
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Abstract

We present a quantitative analysis of small RNA dynamics during the transition from hPSCs to the three germ layer lineages to identify spatiotemporal-specific small RNAs that may be involved in hPSC differentiation. To determine the degree of spatiotemporal specificity, we utilized two algorithms, namely normalized maximum timepoint specificity index (NMTSI) and across-tissue specificity index (ASI). NMTSI could identify spatiotemporal-specific small RNAs that go up or down at just one timepoint in a specific lineage. ASI could identify spatiotemporal-specific small RNAs that maintain high expression from intermediate timepoints to the terminal timepoint in a specific lineage. Beyond analyzing single small RNAs, we also quantified the spatiotemporal-specificity of microRNA families and observed their differential expression patterns in certain lineages. To clarify the regulatory effects of group miRNAs on cellular events during lineage differentiation, we performed a gene ontology (GO) analysis on the downstream targets of synergistically up-and downregulated microRNAs. To provide an integrated interface for researchers to access and browse our analysis results, we designed a web-based tool at https://keyminer.pythonanywhere.com/km/.

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  • https://keyminer.pythonanywhere.com/km/

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 27, 2019.
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Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond
Lu Li, Jin Feng Li, Dan Dan Cao, Vassilios Papadopoulos, Wai Yee Chan
bioRxiv 784819; doi: https://doi.org/10.1101/784819
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Analysis of spatiotemporal specificity of small RNAs regulating hPSC differentiation and beyond
Lu Li, Jin Feng Li, Dan Dan Cao, Vassilios Papadopoulos, Wai Yee Chan
bioRxiv 784819; doi: https://doi.org/10.1101/784819

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