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 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:Goal of the study was to compare single cell (sc) and single nucleus (sn) sequencing of murine kidney after mild (17min) and severe (27min) ischemia reperfusion injury
Project description:The study used a clinically relevant mouse model of chronic aristolochic acid nephropathy (AAN) to investigate the responses of proximal tubular cells during kidney fibrosis by single-nucleus RNA sequencing. The experiment involved 4 mice with AAN induced chronic renal fibrosis and 4 naive controls.
Project description:The kidney is composed of > 40 cell types that work collectively to maintain fluid-electrolyte balance. If not enough fluid is consumed to remain in balance, then vasopressin is released and acts in the kidney to increase water reabsorption. Here the authors used kidney single nucleus multiome-sequencing to determine cell-specific transcriptomes and chromatin accessibility profiles of male and female control (ad libitum water and food) or mildly dehydrated mice (ad libitum food, water deprivation). There were hundreds of sex- and dehydration-specific differentially expressed genes throughout the kidney, most of which did not have a significant change in chromatin accessibility. Thus, even mild dehydration causes cell- and sex-specific transcriptomic changes even though the kidney function to conserve water is the same.