title: GSM7321069: Chronic Kidney Disease, CKD_1, snATACseq; Homo sapiens; ATAC-seq
library_construction_protocol: For single nucleus multiomes, samples were cut into < 2 mm pieces and homogenized using a Dounce homogenizer with the loose head pestle (885302-0002; Kimble Chase) in 2 ml of Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) with protease inhibitor (5892791001; Roche) at 4°C. Samples were then filtered through a 200μm cell strainer (43-50200; pluriSelect) and homogenized in a Dounce homogenizer with the tight head pestle. Samples were incubated on ice for 5 minutes in 4 ml of EZ Lysis buffer, then filtered through a 40μm cell strainer (43-50040; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The resuspended pellet was then washed with 4ml of lysis buffer and incubated for 5 minutes at 4°C. The sample was centrifuged again and resuspended in Diluted Nuclei Buffer (PN-2000153; 10X Genomics) and filtered through a 5μm cell strainer (43-50005; pluriSelect). After counting, nuclei suspensions were diluted as needed to target 10,000 nuclei per lane and loaded into a thermal cycler to begin the transposition reaction. The manufacturer's protocol was followed for the completion of library preparation. For snATAC-seq, samples were chopped into < 2 mm pieces, homogenized with a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) with protease inhibitor (5892791001; Roche) and incubated on ice for 5 min. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500 × g for 5 min at 4 °C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 min. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10 × Genomics, PN-2000153). The suspension was then filtered through a 5-μm cell strainer (43-50005-03, pluriSelect) and counted. After counting, nuclei suspensions were diluted to target 10,000 nuclei per lane and loaded into a thermal cycler to begin the transposition reaction. The manufacturer's protocol was followed for the completion of library preparation. Libraries were generated according to the manufacter's instructions for either single cell multiome ATAC + gene expression OR single cell ATAC. single cell multiome ATAC + gene expression OR single cell ATAC sequencing