GSM9576439: Rat cortex, TBI + ELV biological rep 2, snATAC; Rattus norvegicus; ATAC-seq
Lesional cortex from Sham, Veh, and ELV rats was dissected and snap-frozen at –80°C. More information about the tissue dissection can be found in Supplementary Fig. 8C. The tissue was thoroughly homogenized, and single-nuclei were isolated using the 10x Genomics protocol (Pleasanton, CA, CG000505). The protocol involved lysis and dissociation of the tissue, followed by filtration on the Nuclei Isolation Column using centrifugation. Nuclei were resuspended in 50 µL of resuspension buffer with debris removal buffer to ensure purity. Nuclei concentration was determined with a Luna-FL cell counter (Logos Biosystems, Annandale, VA). Using the 10x Genomics Chromium Controller, RNA and ATAC libraries were generated on a cell-by-cell basis using microfluidic partitioning to capture single cells and prepare barcoded, next-generation sequencing (NGS) libraries. All samples were processed in the same batch. The pooled mRNA and ATAC libraries from all 6 samples were sequenced separately with a NextSeq 2000 system using two flow cells (one for ATAC and one for mRNA) (Illumina, San Diego, CA), targeting a minimum of 20,000 read pairs per cell for the mRNA library and 25,000 read pairs per cell for the ATAC library.