GSM8723671: Mouse_Small-Intestine_scATAC-Seq; Mus musculus; ATAC-seq
Nuclei were isolated from fresh-frozen tissue samples of nine murine organs using a protocol optimized for each tissue type. The process included tissue homogenization in cold homogenization buffer, filtration through cell strainers, and density gradient centrifugation using OptiPrep solutions. Isolated nuclei were checked for integrity using SYBR Green staining and counted before proceeding to single-cell library preparation. Single-cell libraries were prepared using the Chromium Single Cell ATAC reagent kit v1.1 (10x Genomics) following the manufacturer's guidelines. Approximately 10,000 nuclei per sample were subjected to transposition using Tn5 transposase, followed by partitioning into GEMs using the Chromium Controller. After barcoding and amplification of DNA fragments, libraries were purified, indexed, and size-selected for high-throughput sequencing. Quality control was performed using Agilent Bioanalyzer and KAPA Library Quantification kits.