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Studies were incorporated in a barcode, matrix, feature format. This format can be found on the
10x Genomics website
for processing of single cell studies to obtain the gene expression matrices.
For each study, the metadata incorporated in GEO were manually curated into profiles and the samples were separated based on applicable groups and conditions.
The expression data from the cells for the samples within the same profile and condition were aggregated into an expression matrix with the cell barcodes having the sample name appended to it to ensure unique cell names.
Description (from GEO)
Submission Date: Dec 28, 2020
Summary: β cell proliferation rates decline with age and adult β cells have limited self-duplicating activity for regeneration, which predisposes to diabetes. Here we show that, among MYC family members, Mycl was expressed preferentially in proliferating immature endocrine cells. Genetic ablation of Mycl caused a modest reduction in cell proliferation of pancreatic endocrine cells in neonatal mice. By contrast, systemic expression of Mycl in mice stimulated proliferation in pancreatic islet cells and resulted in expansion of pancreatic islets without forming tumors in other organs. Single-cell RNA sequencing and genetic tracing experiments revealed that the expression of Mycl provoked transcription signatures associated with immature proliferating endocrine cells and stimulated self-duplication in adult hormone-expressing cells. The expanded hormone-expressing cells ceased proliferation but persisted after withdrawal of Mycl expression. Remarkably, a subset of the expanded α cells gave rise to insulin-producing cells after the withdrawal. Moreover, transient Mycl expression in vivo was sufficient to normalize increased blood glucose levels in diabetic mice evoked by chemical ablation of β cells. In vitro expression of Mycl similarly provoked active replication without inducing apoptosis in adult hormone-expressing islet cells, even those from aged mice. Furthermore, the expanded islet cells functioned in diabetic mice after transplantation. Finally, we show that MYCL stimulated self-duplication of human adult cadaveric islet cells. Collectively, these results demonstrate that sole induction of Mycl expands adult β cells both in vivo and in vitro. Moreover, islet cell-specific reprogramming via transient Mycl transduction elicits endogenous expansion of insulin-producing cells in adult pancreas through both self-duplication of β cells and transdifferentiation ofα cells into insulin-producing cells, which may provide a regenerative strategy of β cells.
GEO Accession ID: GSE163947
PMID: No Pubmed ID
Preprocessing and downstream analysis were computed using the scanpy Python library and the
steps of processing followed the Seurat vignette. Cells and genes with no expression or very low expression were
removed from the dataset based on a predefined threshold. The data was then normalized across the expression within the cells and log normalized. The top 2000 highly variable genes were extracted to be used for downstream analysis.
For each of these aggregated data matrices, the clusters were computed using the leiden algorithm. Scanpy was then used to compute the PCA, t-SNE, and UMAPs.
The points in the plots are labelled by their corresponding cell type labels. The cell type labels were computed using the wilcoxon method as the differential gene expression method.
The top 250 genes were then used for enrichment analysis against the CellMarker library in order to determine the most appropriate cell type label with the lowest p-value.
Select conditions below to toggle them from the plot:
| Cell Types | Cell Samples |
|---|---|
Differential gene expression can be computed for a single cell type labeled group of cells vs the rest.
These include wilcoxon,
DESeq2, or characteristic direction.