Project description:To better understand the underlying mechanism of beta-cell regeneration in adult zebrafish, we performed single-cell transcriptomic profiling of the pancreatic tissue (using 10X Genomics) at various stages post beta-cell ablation.
Project description:The pancreatic beta-cells regulate blood glucose levels by secreting the hormone insulin in response to increasing glucose levels. Recent work has identified molecular and functional heterogeneity among the beta-cell community. To ontain an unbiased picture into the molecular heterogeneity present in zebrafish pancreatic cells, we performed droplet based next-generation sequencing of individual pancreatic cells. Using unsupervised clustering, we could identify all the major cell types present in the pancreas. Moreover, we could define sub-populations within the major cell-types, demonstrating the presence of molecular heterogeneity within nominally homogenous cell-populations.
Project description:Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. Using a pancreatic cancer mouse model, we applied a microfluidic device to isolate CTCs independently of tumor epitopes, subjecting these to single cell RNA-sequencing. This study was conducted to determine the heterogeneity of pancreatic CTCs and to compare these CTCs to matched primary tumors, cell line controls (NB508 cancer cell line and MEF non-cancer cell line), primary tumor single cells, and normal leukocytes/WBCs. We profiled RNA from 75 single cells circulating in mouse blood enriched for circulating tumor cells from 5 mice, 12 single cells from a mouse embryonic fibroblast cell line, 16 single cells from the nb508 mouse pancreatic cancer cell line, 12 single mouse white blood cells, 18 single GFP lineage-traced circulating tumor cells from two mice, 20 single GFP lineage-traced cancer cells from the primary pancreatic tumor of a mouse, and 34 dilutions to 10 or 100 picograms of total RNA from mouse primary pancreatic tumors from 4 mice.
Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide (GO) on the (innate) immune system using zebrafish as a model. We previously performed single-cell RNA-sequencing of germ-free zebrafish embryos exposed to GO plus the microbial metabolite butyrate (BA). Here, we performed a follow up experiment using germ-free lck-GFP transgenic fish in which the zebrafish were exposed to GO plus BA at 5 dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single-cell RNA-sequencing using 10x Genomics.
Project description:The present study was conducted in the frame of the EU-funded Graphene Flagship project. We previously evaluated the impact of graphene oxide (GO) on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild-type versus AhR-deficient zebrafish. Here, we performed single-cell RNA-sequencing (10x Genomics) on whole (dissociated) germ-free (GF) zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.
Project description:Pancreatic beta-calls are responsible for regulating the blood glucose levels via secretion of hormone insulin. To elucidate the chromatin state in zebrafish beta-cells, we performed ATAC-Sequencing.
Project description:Circulating Tumor Cells (CTCs) are shed from primary tumors into the bloodstream, mediating the hematogenous spread of cancer to distant organs. Using a pancreatic cancer mouse model, we applied a microfluidic device to isolate CTCs independently of tumor epitopes, subjecting these to single cell RNA-sequencing. This study was conducted to determine the heterogeneity of pancreatic CTCs and to compare these CTCs to matched primary tumors, cell line controls (NB508 cancer cell line and MEF non-cancer cell line), primary tumor single cells, and normal leukocytes/WBCs.