title: 6 week sample C
design: All electrodes used for this study were single-shank, silicon, Michigan-style  microelectrodes (A1x16-3mm-100-703-CMLP, 15 um thickness, NeuroNexus Inc, AnnArbor,  MI). Adult, male, Sprague Dawley rats received implants in motor cortex using coordinates and  procedures as previously described]. Briefly, electrodes were inserted (+3.0mm AP,  2.5mm ML from Bregma, 2.0 mm deep) during isoflurane anesthesia, and the surgical site was  closed via a dental acrylic headcap. Post-operative analgesia was achieved with injected  meloxicam (2mg/kg) and topical application of bupivacaine. At the appropriate timepoint (24  hours, 1 week, or 6 weeks), animals were euthanized via sodium pentobarbital administration  and decapitation, and brains were rapidly removed and cryo-embedded using liquid nitrogen (n=3 rats/time point). Aligning with other studies using this ST method, animals were  not perfused prior to euthanasia. Tissue was then cryosectioned from primary motor cortex at a  depth of ~1000m and mounted on a Visium Spatial Gene Expression slide (10x Genomics,  Pleasanton CA). All animal procedures were approved by the Michigan State University Animal  Care and Use CommitteeSamples were transferred to the University of Michigan Advanced Genomics core for library preparation and sequencing. cDNA quality was assessed using the Tapestation 2200 (Agilent) and subjected to library preparation following the manufacturers protocol (10x Genomics). Final library quality was assessed using the LabChip GX (PerkinElmer). Pooled libraries were subjected to paired-end sequencing according to the manufacturers protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de_x0002_multiplexed Fastq files and the SpaceRanger Pipeline (version: 2.0.0, 10x Genomics) was used to align reads and generate count matrices