KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-beta amyloid (1:300; IHC) | Thermo Fisher Scientific | Cat#71-5800; RRID: AB_2533989 |
| Mouse anti-Phospho-Tau (Ser202, Thr205) (AT8) (1:1000; IHC) | Thermo Fisher Scientific | Cat#MN1020; RRID: AB_223647 |
| Rat anti-Bromodeoxyuridine/BrdU (BU1/75 (ICR1)) (1:500; IHC) | Novus Biologicals | Cat#NB500-169; RRID: AB_10002608 |
| Rat anti-mouse CD11b (1:500; IHC) | Bio-Rad | Cat#MCA711GT; RRID: AB_1100616 |
| Mouse anti-Iba1 (1:500; IHC) | Wako | Cat#016-26721; RRID: AB_2811160 |
| Rat anti-Mouse CD68 (1:500; IHC) | Bio-Rad | Cat#MCA1957GA; RRID: AB_324217 |
| Biotinylated goat anti-rabbit IgG (for beta amyloid, 1:500; IHC) | Vector Laboratories | Cat#BA-1000; RRID: AB_2313606 |
| Biotinylated horse anti-mouse IgG, rat adsorbed (for AT8 and Iba1, 1:500; IHC) | Vector Laboratories | Cat#BA-2001; RRID: AB_2336180 |
| Biotin-SP-AffiniPure donkey anti-rat IgG (H+L) (for BrdU, 1:250; IHC) | Jackson ImmunoResearch | Cat#712-065-150; RRID: AB_2340646 |
| Donkey anti rat IgG (H+L), biotin (for CD11b, 1:250; IHC) | Thermo Fisher Scientific | Cat#A18743; RRID: AB_2535520 |
| Rat anti-Ki-67 Monoclonal Antibody (SolA15) (1:200; IHC) | Thermo Fisher Scientific | Cat#14-5698-82; RRID: AB_10854564 |
| Rabbit anti-SOX2 (1:200; IHC) | Abcam | Cat#ab97959; RRID: AB_2341193 |
| Mouse anti-GFAP (1:200; IHC) | Cell Signaling | Cat#3670; RRID: AB_561049 |
| Donkey anti-rat-488 (for BrdU, Ki67 and GFAP, 1:400; IHC) | Thermo Fisher Scientific | Cat#A-21208; RRID: AB_2535794 |
| Donkey anti-rabbit-594 (for Sox2, 1:400; IHC) | Thermo Fisher Scientific | Cat#A-21207; RRID: AB_141637 |
| Rat anti-mouse CD11b antibody (1 μg/μL; IP) | Bio-Rad | Cat#MCA711GT; RRID:AB_321292 |
| Rabbit anti-NOX2 (1:5000; WB) | Abcam | Cat#ab129068; RRID: AB_11144496 |
| Rabbit anti-Aβ42 (1:500; WB) | Abcam | Cat#ab201060; RRID: AB_2818982 |
| Mouse anti-Vinculin (1:1000; WB) | Millipore | Cat#MAB3574; RRID: AB_2304338 |
| Chemicals, peptides, and recombinant proteins | ||
| Paraformaldehyde | Sigma-Aldrich | Cat#158127; CAS:30525-89-4 |
| 5’-Bromo-2’-deoxyuridine (BrdU) | Sigma-Aldrich | Cat#B5002; CAS:59-14-3 |
| Normal Donkey Serum | Jackson ImmunoResearch | Cat#017-000-121 |
| Polyvinyl alcohol mounting medium with DABCO, antifading | Sigma-Aldrich | Cat#10981 |
| Hoechst 33342 Solution | Thermo Fisher Scientific | Cat#62249 |
| VECTASHIELD® HardSet™ Antifade Mounting Medium with DAPI | Vector Laboratories | Cat#H-1500 |
| RIPA Lysis and Extraction Buffer | Thermo Fisher Scientific | Cat#89900 |
| DAB (3,3’-diaminobenzidine) Peroxidase (HRP) Substrate Kit, With Nickel | Vector Laboratories | Cat#SK-4100 |
| Apocynin | Sigma-Aldrich | Cat#178385; CAS:498-02-2 |
| VECTASTAIN® Elite Avidin-Biotin Complex (ABC)-HRP Detection Kit, Peroxidase (Standard) | Vector Laboratories | Cat#PK-6100 |
| NuPAGE™ LDS Sample Buffer (4X) | Invitrogen | Cat#NP0007 |
| HyGLO™ Chemiluminescent HRP Detection Reagent | Denville Scientific | Cat#E2500 |
| RNase-Free DNase Set | Qiagen | Cat#79254 |
| Papain, Lyophilized | Worthington Biochemical | Cat#LS003118; CAS: 9001-73-4 |
| HiLyte™ Fluor 555-labeled Amyloidβ 42 (Aβ42) | AnaSpec | Cat#AS-60480-01 |
| Poly-D Lysine | Sigma-Aldrich | Cat#P7280 |
| Percoll PLUS | Cytiva | Cat#17-5445-02 |
| Critical commercial assays | ||
| Dynabeads™ Protein G Immunoprecipitation Kit | Thermo Fisher Scientific | Cat#10007D |
| Rat CYBB / NOX2 / gp91phox ELISA Kit | LSBio | Cat#LS-F39030 |
| V-PLEX Proinflammatory Panel 1 (mouse) Kit | Meso Scale Diagnostics | Cat#K15048D-1 |
| RNeasy Lipid Tissue Mini Kit | Qiagen | Cat#74804 |
| V-PLEX Plus Aβ Peptide Panel 1 (4G8) | Meso Scale Diagnostics | Cat#K15199G-1 |
| D1000 ScreenTape Assay | Agilent Technologies | N/A |
| KAPA mRNA HyperPrep kit | Roche-Sequencing | N/A |
| Deposited data | ||
| RNA-Seq of hemi-cortex of the 8.5 month old 3xTg young mice study | This paper | SRA: PRJNA864838 |
| Barnes Maze data of E4FAD mice | This paper | Mendeley Data: https://doi.org/10.17632/p2c5z4vjsw.1 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| Mouse: 3xTg | Frank LaFerla, University of California, Irvine | N/A |
| Mouse: E4FAD | Mary Jo LaDu, University of Illinois | N/A |
| Mouse: Nox2-KO | The Jackson Laboratory | JAX: 002365 |
| Mouse: 3xTg/Nox2-KO | Generated from 3xTg and Nox2KO | N/A |
| Software and algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| GraphPad Prism v.8 | Graphpad | https://www.graphpad.com/ |
| HTSeq | Anders et al., 2015 | https://htseq.readthedocs.io/en/master/ |
| EdgeR | McCarthy et al., 2012; Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| FastQC v0.11.8 | Andrews, 2010 | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Trimmomatic v0.38 | Bolger et al., 2014 | http://www.usadellab.org/cms/index.php?page=trimmomatic |
| STAR v2.6.1d | Dobin et al., 2013 | http://code.google.com/p/rna-star/ |
| gProfileR v0.6.8 | Reimand et al., 2007 | http://biit.cs.ut.ee/gprofiler/ |
| Imagelab 6.0 software | Bio-Rad | https://www.bio-rad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z |
| Other | ||
| Mouse diet: Fasting mimicking diet (FMD) | Cheng et al., 2017 | N/A |
| Mouse diet: 4% protein-restricted diet (4% PR) | Parrella et al., 2013 | N/A |
| Human diet: ProlonAD TM | Propriety formulation belonging to L-Nutra | https://www.prolon.it |
| Control Diet: PicoLab Rodent Diet 20 | LabDiet | Cat#5053 |
| HydroGel | ClearH2O | N/A |
| Barnes Maze | San Diego Instruments | N/A |
| All-in-One Fluorescence Microscope | Keyence | BZ-X710 |
| Olympus BX50 Microscope | Olympus | N/A |
| Olympus DP73 Camera | Olympus | N/A |
| Zeiss Laser Scanning Microscope-780 upright microscope | Zeiss | N/A |
| 2200 TapeStation | Agilent Technologies | N/A |
| HiSeq3000 | Illumina | N/A |
| Vibratome | Leica | VT1000S |
| Janus G3 liquid handler | Perkin-Elmer | N/A |