| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Goat anti-rabbit secondary, HRP, ready to use | Agilent Technologies | Cat# K400311-2 |
| Rabbit anti-brevican (BCAN), 1:2,000 | Abcam | Cat# ab285162 |
| Rabbit anti-CD68, 1:400 | Abcam | Cat# ab125212; RRID: AB_10975465 |
| Rabbit anti-ferritin (FTH1), 1:300 | Cell Signaling Technology | Cat# 4393; RRID: AB_11217441 |
| Rabbit anti-myelin proteolipid protein (PLP), 1:500 | Abcam | Cat# ab28486; RRID: AB_776593 |
| Rabbit anti-NeuN, 1:3,000 | Abcam | Cat# ab177487; RRID: AB_2532109 |
| Rabbit anti-neurofilament 200 (NF), 1:2,000 | Sigma-Aldrich | Cat# N4142; RRID: AB_477272 |
| Chemicals, peptides, and recombinant proteins | ||
| Antibody diluent, background reducing | Agilent Technologies | Cat# S302283-2 |
| Citroclear | Genta Medical | Cat# CITO50 |
| DPX | Sigma-Aldrich | Cat# 1005790500 |
| Ethanol absolute | Sigma-Aldrich | Cat# 32221-M |
| Fluorinert | Acota | Cat# FC-770 |
| Gadovist (gadolinium-based contrast agent) | Bayer | Cat# 30351004 |
| Harris hematoxylin | Leica Biosystems | Cat# 3801560E |
| Heparin | Wockhardt | Cat# 30170145 |
| Histoplast PE paraffin wax | SLS Ltd. | Cat# HIS3324 |
| Hydrochloric acid 37% (HCl) | VWR | Cat# 20252.244 |
| Hydrogen peroxide 30% (H2O2) | Fisher Scientific | Cat# 10687022 |
| Industrial denatured alcohol (IDA) | Genta Medical | Cat# I99050 |
| Ketamidor (ketamine) 100 mg/mL solution for injection | Chanelle Pharma | Cat# 30395940 |
| Mollifex | VWR | Cat# 360584X |
| Oxoid phosphate-buffered saline (PBS) tablets | Thermo Scientific | Cat# BR0014g |
| Paraformaldehyde (PFA) | Electron Microscopy Sciences | Cat# 15710 |
| Protein block, serum free | Agilent Technologies | Cat# X090930-2 |
| Sodium azide | Sigma-Aldrich | Cat# S2002 |
| Sodium chloride | Fisher Scientific | Cat# 10316943 |
| Sodium hydroxide 2 mol/L (2 N) in aqueous solution (NaOH) | VWR | Cat# 98108.290 |
| Tri-sodium citrate dihydrate (citrate) | Fisher Scientific | Cat# 10396430 |
| Tris (hydroxymethyl) methylamine (Tris buffer) | Fisher Scientific | Cat# 10785341 |
| Triton X | Sigma-Aldrich | Cat# X100 |
| Xylazine | Bayer | Cat# 2150569 |
| Xylene | Genta Medical | Cat# XYL050 |
| Critical commercial assays | ||
| Liquid DAB+ Substrate Chromogen System Kit |
Agilent Technologies | Cat# 346811-2 |
| Experimental models: Organisms/strains | ||
| Mouse, Bcan knockout (BCAN-DEL465-EM1-B6N-IC) and wild-type littermates, 10 weeks, males and females | MRC Harwell | N/A |
| Mouse, FUSΔ14/Δ14 and wild-type littermates (C57BL/6J-DBA/2J genetic background), 12 weeks old, females | MRC Harwell6 | N/A |
| Mouse, SOD1-G93A, 18 weeks, males and females | MRC Harwell | N/A |
| Mouse, Tardp-M323K and wild-type littermates, 12 months old, females | MRC Harwell7 | N/A |
| Mouse, Vcan point mutation (VCAN-E441A-EM2-B6-IC) and wild-type littermates, 10 weeks, males and females | MRC Harwell | N/A |
| Software and algorithms | ||
| Fiji ImageJ | National Institutes of Health8 | RRID: SCR_003070 https://imagej.net/software/fiji/ |
| FMRIB Linear Image Registration Tool (FLIRT) | University of Oxford | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT |
| FMRIB Software Library (FSL) | University of Oxford9 | RRID: SCR_002823 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ |
| FSLeyes | University of Oxford | https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes |
| Ihcpy (SAF; stained area fraction maps) | University of Oxford | https://git.fmrib.ox.ac.uk/spet4877/ihcpy/-/tree/main/ |
| TIRL (version 3) | University of Oxford | https://git.fmrib.ox.ac.uk/ihuszar/tirl/-/tree/v3 |
| TIRLscripts | University of Oxford | https://git.fmrib.ox.ac.uk/ihuszar/tirlscripts/-/tree/master/tirlscripts/oxford/mouse |
| Other | ||
| Automatic tissue processor | Thermo Scientific | STP120 |
| Benchtop autoclave | Astell Scientific | AMB230BT |
| Brain matrix (mouse coronal 40–75 g) | Electron Microscopy Sciences | Cat# 69080-C |
| Brush 2.5 mm diameter | Scientific Laboratory Supplies | Cat# BRU2054 |
| Coverslip glass 24 × 50 mm | VWR | Cat# 631-0146 |
| Microscope | Olympus | BX43 |
| Microtome blades, S35 fine, high-profile | VWR | Cat# 720-1998 |
| Microwave | Russell Hobbs | RHM2077 |
| Razor blade | Azpack | Cat# 11904325 |
| Rotary microtome | Leica Biosystems | RM2135 |
| ScanScope slide scanner | Leica Biosystems | AT Turbo |
| Shandon Plastic Coverplates | Epredia | Cat# 72110017 |
| Shandon Sequenza Immunostaining Center Slide Rack | Epredia | Cat# 73310017 |
| Stainless steel histology mold 37 × 24 × 9 mm | CellPath | Cat# GBB-3714-05A |
| Stainless steel histology mold 60 × 45 × 15 mm (Supa Mega) | CellPath | Cat# GBC-6014-05A |
| SuperFrost Plus adhesion slides | Epredia | Cat# J1800AMNZ |
| Tissue embedding system | Thermo Scientific | HistoStar |
| Tissue embedding cassette | Kartell | Cat# 0292503 |
| Tweezers/forceps, blunt | Fisher Scientific | Cat# 15576579 |
| Tweezers/forceps, sharp | Fisher Scientific | Cat# 12381369 |
| Warming oven | Memmert | D 06060 model 400 |
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