GSM9168619: scATAC-seq Sample 3 Tau 20mo; Rattus norvegicus; ATAC-seq
Hippocampus from 10-month and 20-month-old female McGill-R955-hTau transgenic rat and age-matching WT controls were dissected and snap-frozen at -80°C until further use. The tissues were minced and homogenized, and single-nuclei were isolated following 10x Genomics protocol (Pleasanton, CA, CG000505). Briefly, frozen tissues were minced, lysed, and dissociated in lysis buffer and then filtered on Nuclei Isolation Column by centrifugation. Nuclei pellets were washed with debris removal buffer, and nuclei were resuspended with 50 µL resuspension buffer. Nuclei concentration was determined with Luna-FL cell counter (Logos Biosystems, Annandale, VA). For tissues used for Spatial sequencing: 10-month and 20-month-old females McGill-R955-hTau transgenic rat and age-matching WT controls were perfused with 10% formalin, and the fixed brains were embedded in OCT compound, coronally sectioned at 10 µm using CryoStar NX50 cryotome (Epredia Kalamazoo, MI) and mounted onto microscope slides. Tissue sections were transferred onto the fiducial frames of a Visium Spatial Gene Expression slide (PN-2000233, 10x Genomics, Pleasanton, CA) using the Visium CytAssist. Using the 10x Genomics Chromium Controller and following downstream protocols, 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. The mRNA and ATAC libraries were sequenced using a NovaSeq 6000 system (Illumina, San Diego, CA) targeting at minimum 80,000 and 50,000 reads per cell for mRNA and ATAC, respectively.  For spatial sequencing: The tissues underwent spatial barcoding, and cDNA library was generated from the tissue mRNA as outlined in the Visium Spatial Gene Expression User Guide (CG000239, 10x Genomics). The mRNA transcriptome was mapped to a 55 µm spatial resolution, corresponding to 1-10 cells per spot. The mRNA library was sequenced using a Nextseq 2000 platform.