Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq

ABSTRACT: Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform. Total 213 H1 single cells and 247 H1-Fucci single cells were sequenced. The 213 H1 cells were used to evaluate Oscope in identifying oscillatory genes. The H1-Fucci cells were used to confirm the cell cycle gene cluster identified by Oscope in the H1 hESCs.

ORGANISM(S): Homo sapiens

SUBMITTER: Ning Leng

PROVIDER: E-GEOD-64016 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Mesenchymal stem/stromal cells (MSCs) are multipotent cells that can differentiate into a variety of cell types forming connective tissue and skeleton, and are essential participants in the development of all organs. However, MSC precursors remain largely unknown. In human embryonic stem cells (hESCs) directed to mesendodermal differentiation through coculture with OP9 stromal cells, we identified a population of mesodermal cells by surface expression of apelin receptor (APLNR1). APLNR+ cells were enriched with precursors generating compact spheroid colonies in semisolid suspension culture. Being formed by single cells, these colonies consisted of a uniform population of mesenchymal cells with a transcriptional profile representative of embryonic mesenchyme originating from lateral plate/extraembryonic mesoderm. Mesenchymal colony formation required serum-free medium and FGF2 as a colony-forming factor, could be significantly enhanced by PDGF-BB, but suppressed by VEGF. When transferred to the adherent cultures in serum-free medium with FGF2, individual colonies gave rise to multipotential mesenchymal cell lines with typical phenotype (CD146+CD105+CD73+CD31-CD43-CD45-), differentiation (chondro-, osteo-, and adipogenesis) and proliferation (>80 doublings) potentials. Consistent with lineage-restricted differentiation pattern, neither endothelial nor hematopoietic cells could be produced from adherent mesenchymal cultures, however endothelial cells could be derived from mesenchymal colonies in the early days of colony-forming culture suggesting that mesenchymal cells arose from cells with primary angiogenic potential (mesangioblasts). Together these studies identified mesangioblasts as the earliest clonogenic mesenchymal precursors at this stage of their specification from mesoderm. This set (11 samples) of expression data is sequential stages of MSC development from hESCs (H1), namely ALPNR+ mesodermal precursors isolated on day 2 and day 3 differentiation, mesangioblast (MB) cores (Day 2 H1-derived cores), hemangioblast (HB) cores (day 3 H1-derived cores), mesangioblast (MB) and hemangioblast (HB) colonies, and colony-derived MSC lines at passage 1 and 5.

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Single cell RNA-seq data of human hESCs to evaluate Oscope - a statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-Seq

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