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

By Lu Li, Jin Feng Li, Dan Dan Cao, Vassilios Papadopoulos, Wai Yee Chan

Posted 27 Sep 2019
bioRxiv DOI: 10.1101/784819

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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