title: GSM7883316: KO IL, replicate 1, scRNAseq; Mus musculus; RNA-Seq
library_construction_protocol: Single-cell RNA sequencing and bioinformatic analysis were performed in white matter tissues dissected from the WT or Nhe1 cKO brains at 3 days post-tMCAO. Briefly, mice were euthanized with an overdose of CO2 and transcardially perfused with ice-cold saline, as described before (10). The brains were dissected and cut into 4 coronal slices of 2 mm thickness in a brain slicer matrix. Cortices were removed and white matter tissues (corpus callosum and external capsules) were separated from the contralateral and ipsilateral hemispheres and dissociated into single-cell suspensions using a Neural Tissue Dissociation Kit with the gentleMAC Octo Dissociator (Miltenyi Biotech Inc., Germany). Myelin was removed using the 30/70 Percoll gradient method as described (10). Single-cell suspension was prepared as we described before 13 and used for droplet-based scRNAseq (10x Genomics). The quality of the single-cell suspension was confirmed prior to the start of library preparation with an acridine-orange-propidium iodide stain (Nexcelcom Biosciences) and a Cellometer Auto 2000 Viability Counter (Nexcelcom Biosciences). Library Preparation (Chromium Next GEM Single Cell 3' Reagent kit v3.1) was conducted as per the manufacturer's protocol. The quality of the cDNA libraries was verified using a High Sensitivity D5000 ScreenTape and 4200 Tapestation system (Agilent Technologies).