title: GSM8888333: Ctrl_GEX; Mus musculus; RNA-Seq
library_construction_protocol: Immediately following euthanasia, mice were transcardially perfused (10mL DPBS), and brains were removed and placed in iMED+ (15mM HEPES and 0.6% glucose in HBSS with phenol red). Dura, lesion, and perilesional cortex were dissected and processed separately. Tissue from male and female mice within experimental conditions were combined. Tissue was minced for 10 minutes in 100mL of TST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, and 0.01% BSA in nuclease-free water), followed by filtration (40mm), and washing with TST and ST buffer (146 mM NaCl, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, and 21 mM MgCl2). Samples were centrifuged (500g 10 minutes), resuspended (PBS/1% BSA/0.2UmL Protector RNAse inhibitor), filtered (35mm), and counted. A maximum of 2x10^6 nuclei were multiplexed and washed (CellPlex, 10X Genomics), per manufacturer's instructions.  Immediately before sorting, multiplexed microanatomical regions (lesion, parenchyma, and dural meninges) from individual mice were combined at desired ratios (75% lesion, 25% parenchyma). Nuclei were subsequently sorted (FSC/SSC/DAPI). All samples were centrifuged (500g 15 minutes) and resuspended to a maximum of 16,500 nuclei in 50uL. Up to 1.6 x 10^4 nuclei were loaded onto the Chromium Controller (10X Genomics). Chromium Single Cell 3' v3.1 reagents were used for library preparation according to the manufacturer's protocol.