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:We performed single nucleus RNA sequencing (snRNA-seq) and assay for transposase-accessible chromatin with sequencing (snATAC-seq) to map the epigenetic and gene expression signatures of human kidney organoids during the organoid differentiation time course.
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: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:Here, we used joint single-nuclei RNA-sequencing (snRNA-seq) and single-nuclei ATAC sequencing (scATAC) to profile freshly isolated crypts from the human fetal intestine and matched intestinal epithelial only organoids (also known as enteroids) derived from these crypts after one passage of in vitro growth. Organoids were grown in the standard 25% LWRN media with either 100 ng/ml of EGF or 1 ng/ml of EREG added. Fresh crypts were not placed in culture but rather immediately frozen for multiomic processing.