Project description:We analyzed single cell transcriptomes over 80,000 cells isolated from 65 organoids differentiated from iPSCs and ESCs using two different protocols. We find that both protocols generate kidney organoids that contain a diverse range of kidney cells at differing ratios as well as non-renal cell types. We reconstructed lineage relationships during organoid differentiation through pseudotemporal ordering, and identified transcription factor networks associated with fate decisions. When comparing to adult human kidney, we reveal immaturity of all kidney organoid cell types. These results define impressive kidney organoid cell diversity, identify incomplete differentiation as a major roadblock for current directed differentiation protocols and provide a human adult kidney snRNA-seq dataset against which to benchmark future progress.
Project description:In this study, we generated a single nucleus multiomic (snRNA-seq and snATAC-seq) dataset of adult human kidney. We developed a bioinformatic tool to analyze this dataset by identifying key cis-regulatory elements and transcription factors associated with specific cell types and states. We applied this tool to identify transcription factors implicated in proximal tubule cell injury and failed repair states. We demonstrate this tool can be applied to single cell multiomic datasets to derive insight into cell type- and state-specific gene regulatory networks.
Project description:A key limitation in single cell genomics is generating a high-quality single cell suspension that contains rare or difficult to dissociate cell types and is free of RNA degradation or transcriptional stress responses. Samples with unpredictable availability or that must be collected at several timepoints present additional challenges. Using adult mouse kidney, we compared single-cell RNA sequencing (scRNA-seq) data generated using DropSeq with snRNA-seq data generated from nuclei using sNuc-DropSeq, DroNc-seq and 10X Chromium. We validated snRNA-seq on fibrotic kidney from day 14 unilateral ureteral obstruction (UUO).
Project description:We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney with autosomal dominant polycystic kidney disease. snATAC-seq on 5 samples (control1/2/3/4/5) were already done and deposited on GSE151302 as Healthy1-5 (GSM4572187-4572191, respectively)
Project description:Recent advances in single-cell transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. Here, we utilized massively parallel single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally-distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune cell deficiencies within prkdcD3612fs, il2rgaY91fs and double homozygous mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types including two classes of natural killer immune cells, classically-defined and erythroid-primed hematopoietic stem and progenitor cells, mucin secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first comprehensive single cell transcriptomic analysis of kidney and marrow cells in the adult zebrafish.
