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Antibodies
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| Anti-Iba1 Rabbit antibody |
FUJIFILM Wako Shibayagi |
Cat# 019-19741; RRID:AB_839504 |
| Anti-NeuN Mouse antibody |
Millipore Corp. |
Cat# MAB377; RRID:AB_2298772 |
| Amyloid β (N) (82E1) Anti-Human Mouse IgG MoAb |
Immuno-biological Laboratories |
Cat# 10323; RRID:AB_10707424 |
| Anti-GFAP Rabbit antibody |
Thermo Fisher Scientific Inc. |
Cat# 18-0063; RRID:AB_138737 |
| Goat Anti-Rabbit IgG Antibody (H+L), Biotinylated |
Vector Laboratories |
Cat# BA-1000; RRID:AB_2313606 |
| Horse Anti-Mouse IgG Antibody (H+L), Biotinylated |
Vector Laboratories |
Cat# BA-2000; RRID:AB_2313581 |
| Methoxy-X04 |
Tocris Bioscience |
Cat. No. 4920 |
| Chicken anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 594 |
Thermo Fisher Scientific Inc. |
Cat# A-21201; RRID:AB_2535787 |
| Phospho-Tau (Ser202; Thr205) Monoclonal Antibody (AT8) |
Thermo Fisher Scientific Inc. |
Cat# MN1020; RRID:AB_223647 |
| Chicken anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488 |
Thermo Fisher Scientific Inc. |
Cat# A-21200; RRID:AB_2535786 |
| Anti-Amyloid Precursor Protein; C-Terminal antibody produced in rabbit |
MilliporeSigma |
RRID:AB_258409 |
| Bmi1 (D42B3) Rabbit mAb |
Cell Signaling Technology |
Cat# 5856; RRID:AB_10838137 |
| Goat Anti-Rabbit IgG (H L)-HRP Conjugate |
Bio-Rad |
RRID:AB_11125143 |
| Horse Anti-mouse IgG, HRP-linked Antibody |
Cell Signaling Technology |
Cat# 7076; RRID:AB_330924 |
| Anti-β-Actin Antibody (C4) |
Santa Cruz Biotechnology |
Cat# sc-47778; RRID:AB_626632 |
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Bacterial and virus strains
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Biological samples
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Chemicals; peptides; and recombinant proteins
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Critical commercial assays
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| Applied Biosystems™ High-Capacity cDNA Reverse Transcription Kit |
Thermo Fisher Scientific Inc. |
Cat. No. 43-688-14 |
| RNeasy Lipid Tissue Mini kit |
QIAGEN |
Cat. No. 74804 |
| DAB Substrate Kit; Peroxidase (HRP); with Nickel; (3;3’-diaminobenzidine) |
Vector Laboratories; Inc. |
Cat. No. SK-4100 |
| VECTASTAIN Elite ABC HRP Kit (Peroxidase; Standard) Kit |
Vector Laboratories; Inc. |
Cat. No. PK-6100 |
| V-PLEX Aβ Peptide Panel 1 (6E10) Kit |
https://www.mesoscale.com
|
Cat. No. K15200E |
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Deposited data
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| Raw and analyzed RNA-Seq data |
This Paper |
GEO: GSE236731
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Data S1. Uncropped western blots and data underlying graphs
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This Paper
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N/A
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Experimental models: Cell lines
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Experimental models: Organisms/strains
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| APP23 mice; B6.Cg-Tg(Thy1-APP)3Somm/J |
Jackson Laboratory |
RRID:IMSR_JAX:030504 |
| APP-SAA KI mice; B6.Cg-Apptm1.1Dnli/J |
Jackson Laboratory |
RRID:IMSR_JAX:034711 |
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Oligonucleotides
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Recombinant DNA
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Software and algorithms
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| ImageJ (v1.53t) |
NIH |
RRID:SCR_023336 |
| Clocklab Analysis 6 (v6.1.12) |
ActiMetrics |
RRID:SCR_014309 |
| VitalView |
Starr Life Sciences Corp. |
RRID:SCR_014497 |
| ANY-maze (v4.99) |
Stoelting Co. |
RRID:SCR_014289 |
| El Temps program (v.313) |
A. Diez-Nogura; Barcelona; Spain |
http://www.el-temps.com/principal.html
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| Cran-package fpc (v2.2-10) |
https://cran.r-project.org/
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https://cran.r-project.org/web/packages/fpc/index.html
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| DESeq2 |
https://bioconductor.org/
|
RRID:SCR_015687 |
| HISAT2 |
http://ccb.jhu.edu/software/hisat2/index.shtml
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RRID:SCR_015530 |
| JTK_CYCLE |
https://openwetware.org/wiki/HughesLab:JTK_Cycle
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RRID:SCR_017962 |
| Ingenuity Pathway Analysis |
QIAGEN |
RRID:SCR_008653 |
| Metascape |
Metascape.org
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RRID:SCR_016620 |
| Enrichr |
https://maayanlab.cloud/Enrichr/
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RRID:SCR_001575 |
| DisGeNET |
https://www.disgenet.org/
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RRID:SCR_006178 |
| Rosalind (v3.35.10.0) |
https://www.rosalind.bio/
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RRID:SCR_006233 |
| geNORM |
http://www.bioconductor.org
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RRID:SCR_006763 |
| NormqPCR |
http://www.bioconductor.org
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RRID:SCR_003388 |
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Other
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| nCounter Analysis System |
NanoString Technologies; Inc. |
RRID:SCR_021712 |
| RNAlater Stabilization Solution |
Thermo Fisher Scientific Inc. |
Cat. No. AM7021 |
| AMP-AD Knowledge Portal |
https://adknowledgeportal.synapse.org/
|
RRID:SCR_016316 |
| NovaSeq 6000 Sequencing System |
Illumina; Inc. |
RRID:SCR_016387 |
| NanoZoomer S60 Digital slide scanner |
https://www.hamamatsu.com/
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RRID:SCR_022537 |
| ZEN Digital Imaging for Light Microscopy |
https://www.zeiss.com/
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RRID:SCR_013672 |
| OlyVIA (V3.4.1) |
https://www.olympus-lifescience.com
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RRID:SCR_016167 |
| DISCOVERY WORKBENCH |
https://www.mesoscale.com
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RRID:SCR_019192 |
| Prism 9 |
https://www.graphpad.com/
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RRID:SCR_002798 |
| MESO QuickPlex SQ 120 |
https://www.mesoscale.com
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RRID:SCR_020304 |
| Precision Xtra Blood Glucose and Ketone Monitoring System |
Abbott Laboratories; https://abbottstore.com
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Cat. No. 9881465 |
| Agilent 4200 TapeStation System |
Agilent Technologies; Inc. |
RRID:SCR_019398 |
| TaqMan custom probes |
Thermo Fisher Scientific Inc. |
https://www.thermofisher.com/us/en/home/life-science/oligonucleotides-primers-probes-genes/applied-biosystems-custom-primers-probes.html
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| TaqMan™ Fast Advanced Master Mix |
Thermo Fisher Scientific Inc. |
Cat. No. 44-449-64 |
| LSM 800 confocal microscope |
https://www.zeiss.com/
|
RRID:SCR_015963 |
| SLIDEVIEW VS200 Slide Scanner |
Olympus Life Science |
https://www.olympus-lifescience.com/en/solutions-based-systems/vs200/
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| iBright™ CL1500 Imaging System |
Thermo Fisher Scientific Inc |
Cat. No. A44240CFR |
