Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation ...

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    Apr 05, 2018 · In brief, the Seurat object was generated from digital gene expression matrices. The parameter of “Filtercells” is nGene (2000 to 8800) and transcripts (-Inf to 6e + 05). In the standard pre-processing workflow of Seurat, we selected 8706 variable genes for following PCA. Then we performed cell cluster and t-SNE.

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    May 22, 2019 · A weighted correlation network analysis was done using the WGCNA R package v1.6.6 . Using the function FindVariableGenes from Seurat, we calculated the genes with high variation (dispersion > 0.5) across all the cells in sample HH29, and were subsequently used in WGCNA. WGCNA also identified core gene expression networks expressed in mExN subtypes (M10, M11, and M12) and in mInN subtypes (M12, M13, and M14). These core gene networks likely play fundamental roles in establishing and maintaining the identity and function of the corresponding cell types.

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