GoKawiilMice
All mouse experiments were performed according to protocols approved by the Institutional Animal Care and Use Committees (IACUC) at Korea Advanced Institute of Science and Technology (KAIST) and the Institute for Basic Science (IBS), adhering strictly to ethical guidelines. B6.Cg-Tg(APPswe, PSEN1dE9)85Dbo/Mmjax (APP/PS1) mice and B6.Cg-Tg(APPSwFlLon, PSEN1*M146L*L286V)6799Vas/Mmjax (5×FAD) mice were produced in our laboratory and maintained by breeding with C57BL/6J mice. Mice were housed under a 12 h–12 h light–dark cycle. Both male and female mice were used unless otherwise specified in the figure legends. All mice were randomly assigned to experiments, which were performed by investigators blinded to experimental conditions. Gender was not considered unless explicitly noted in figure legends.
Human tissue sections
Human formalin-fixed paraffin-embedded (FFPE) sections were provided by the SNUH Brain Bank and use of these sections for this study was reviewed and determined to be exempt from review by the Public Institutional Review Board designated by the Ministry of Health and Welfare, Republic of Korea. All procedures involving human-derived materials were conducted in accordance with relevant regulations.
Cell lines
HEK293T cells (ATCC) were used solely for AAV production. Cells were maintained in our laboratory and were not independently authenticated for this study. HEK293T cells were confirmed to be free of mycoplasma contamination.
Antibodies and reagents
The antibodies used and their dilution factor were as follows: anti-S100β (Abcam, ab52642, Synaptic System, 287-004; Aves Labs, S100B-0020; 1:500), anti-IBA1 (Wako, 019-19741; Novus, NB100-1028; 1:500), anti-mCherry (Invitrogen, M11217; Aves Labs, mCherry-0020; 1:1,000), anti-vGLUT1 (Millipore, AB5905; 1:1,000), anti-PSD95 (Invitrogen, 51-6900; 1:500), anti-vGAT (Synaptic System, 131-004; 1:1,000), anti-gephyrin (Synaptic System, 147-008; 1:500), anti-FOS (Cell Signaling, 2250S; Synaptic System, 226-308; Synaptic System, 226-017; 1:500), anti-MEGF10 (Merck, ABC10; 1:500), anti-ERBB4 (Abcam, ab32375; Cell Signaling, 4795T; 1:500), anti-parvalbumin (Swant, GP72; 1:1,000), anti-beta amyloid (BioLegend, 803001; Cell Signaling, 2454S; 1:1,000), anti-GFAP (Abcam, ab4674; 1:1,000), anti-AXL (R&D systems, AF854; 1:100), anti-somatostatin (BMA Biomedicals, T-4103; 1:500), anti-VIP (Synaptic System, 443-005; 1:500), anti-NeuN (Sigma-Aldrich, ABN91; 1:500), anti-cleaved caspase-3 (Cell Signaling, 9661S; 1:500), anti-TREM2 (R&D systems, AF1729; 1:500), anti-HA (Cell Signaling, 3724S; 1:500) and anti-pS6 (Cell Signaling, 2211S; 1:500).
Secondary antibodies: donkey anti-goat IgG (H&L) Alexa Fluor 405 (Abcam, ab175665), donkey anti-goat IgG (H+L) Alexa Fluor 488 (Jackson Laboratory, 705-545-003), donkey anti-chicken DyLight 405-conjugated AffiniPure, donkey anti-chicken IgY (IgG) (H+L) (Jackson Laboratory, 703-475-155), donkey anti-chicken IgG (H+L) Alexa Fluor 488 (Jackson Laboratory, 703-545-155), donkey anti-chicken IgG (H+L) Alexa Fluor 594 (Jackson Laboratory, 709-585-155), donkey anti-rat IgG (H+L) Alexa Fluor 594 (Invitrogen, A-21209), donkey anti-rat IgG (H&L) Alexa Fluor 647 (Abcam, ab150155), donkey anti-rabbit IgG (H&L) Alexa Fluor 405 (Abcam, ab175649), donkey anti-rabbit IgG (H+L) Alexa Fluor 488 (Invitrogen, A-21206), donkey anti-rabbit IgG (H+L) Alexa Fluor 594 (Invitrogen, A-21207), donkey anti-guinea pig IgG (H+L) Alexa Fluor 488 (Jackson Laboratory, 706-545-148), donkey anti-guinea pig IgG (H+L) Alexa Fluor 594 (Jackson Laboratory, 706-585-148), donkey anti-guinea pig IgG (H+L) Alexa Fluor 647 (Jackson Laboratory, 706-605-148), donkey anti-sheep IgG H&L (Alexa Fluor 488) (Abcam, ab150177), donkey anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 (Invitrogen, A-21203). All Alexa-Fluor-488-conjugated secondary antibodies were used at a dilution of 1:1,000, whereas all other secondary antibodies were used at 1:500. The following reagents were used: HistoVT One (Nacalai, 06380-05), CNO (Sigma-Aldrich, C0832-5mg).
Python packages for data analysis
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