GSE195460
Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression
Purpose: Single cell sequencing has advanced our understanding of kidney biology. The goals of this study are to compare single nucleus RNA (snRNA-seq) and single nucleus assay for transposase accessible chromatin sequencing (snATAC-seq) from healthy control donors and donors with type 2 diabetic kidney disease to identify altered signaling pathways and chromatin accessibility patterns observed in diabetic kidney disease. Methods: Nuclear dissociation of human kidney cortex samples was performed on samples obtained from patients undergoing tumor nephrectromy or deceased organ donors. snRNA-seq and snATAC-seq libraries were prepared using 10X Genomics kits according to manufacturers instructions. For this study, two healthy control libraries from one donor were prepared with the following chemistries (1 - single cell 3-prime v3, 1 - single cell ATAC v1) and nine DKD libraries from seven donors were prepared with the following chemistries (2 - single cell 5-prime v2 paired-end, 7 - single cell ATAC v1). Raw data for three healthy control and three DKD snRNA-seq libraries sequenced with single nucleus 5-prime R2 only can be found in GSE13188213. Raw data for two healthy control snRNA-seq sequenced with single nucleus 5-prime paired-end and five snATAC-seq single nucleus ATAC v1 libraries can be found in GSE151302. snRNA-seq and snATAC-seq libraries from these earlier studies were recounted with cellranger (v4.0) or cellranger-atac (v2.0) to provide consistency across processed data files. Overall design: snRNA-seq and snATAC-seq of human kidney cortex from patients with and without type 2 diabetic kidney disease