| Antibodies |
|
|
|
| Goat anti Mouse Alexa Fluor 488 |
ThermoFisher Scientific |
Cat# A-10680, RRID: AB_2534062 |
| Goat anti mouse Alexa Fluor 555 |
ThermoFisher Scientific |
Cat# A32727; RRID: AB_2633276 |
| Goat anti Rabbit Alexa Fluor 488 |
ThermoFisher Scientific |
Cat# A-11008, RRID: AB_143165 |
| Goat anti Rabbit Alexa Fluor 555 |
ThermoFisher Scientific |
Cat# A-21429, RRID: AB_2535850 |
| Goat anti-GFAP |
Abcam |
Cat# ab53554; RRID:AB_880202 |
| Goat anti-Mouse HRP |
KPL |
Cat# 5067205 |
| Goat anti-Rabbit HRP |
KPL |
Cat# 5067202 |
| Mouse anti-β-actin |
Sigma |
Cat# A4700; RRID: AB_476730 |
| Mouse anti-α-synuclein |
BD Biosciences |
Cat# 610787; RRID: AB_398108 |
| Mouse anti-Aβ |
Novus Biologicals |
Cat# NB2-50055AF488 |
| Mouse anti-Aβ [Clone 6E10] |
Biolegend |
Cat#803003; RRID:AB_2564652 |
| Mouse anti-Aβ [Clone MOAB2] |
Abcam |
Cat# ab126649 |
| Mouse anti-humanTau [Clone Tau13] |
Abcam |
Cat# ab19030; RRID: AB_778252 |
| Mouse anti-phosphoS422-Tau |
Custom generated antibody (Grueninger et al., 2010) |
N/A |
| Mouse anti-phosphoSer202-Thr205-Tau [Clone AT8] |
Thermo Fisher Scientific |
Cat# MN1020; RRID: AB_223647 |
| Mouse anti misconformed tau [Clone MC1] |
Custom generated antibody (P. Davies) |
RRID: AB_2314773 |
| Mouse anti-Tau [Clone HT7] |
Thermo Fisher Scientific |
Cat# MN1000; RRID: AB_2314654 |
| Rabbit anti-4HNE |
Abcam |
Cat# ab46545; RRID: AB_722490 |
| Rabbit anti-GATE16 |
MBL |
Cat# PM038; RRID: AB_10210502 |
| Rabbit anti-GFAP |
Dako |
Cat# Z0334; RRID: AB_10013382 |
| Rabbit anti-GFAP |
Abcam |
Cat# ab5804; RRID: AB_2109645 |
| Rabbit anti-Iba1 |
Wako |
Cat#019-19741; RRID:AB_839504 |
| Rabbit anti-K48ubiquitin |
Millipore |
Cat# 05-1307; RRID: AB_1587578 |
| Rabbit anti-K63ubiquitin |
Millipore |
Cat# 05-1308; RRID: AB_1587580 |
| Rabbit anti-LAMP-2A |
ThermoFisher Scientific |
Cat# 512200; RRID: AB_2533900 |
| Rabbit anti-LC3 |
Cell Signaling |
Cat# 2775; RRID: AB_915950 |
| Rabbit anti-LRRK2 |
Abcam |
Cat# ab133518 |
| Rabbit anti-p62 |
EnzoLife Sciences |
Cat# BMLPW98600100; RRID: AB_2052149 |
| Rabbit anti-Parkin |
Millipore |
Cat# ab9244; RRID: AB_570711 |
| Rabbit anti-phosphoT231-Tau [Clone EPR2488] |
Abcam |
Cat#ab151559 |
| Rabbit anti-Tyrosine Hydroxylase |
Abcam |
Cat# Ab112; RRID: AB_297840 |
| Rabbit anti-ubiquitin |
Dako |
Cat# 0458; RRID: AB_2315524 |
| Rabbit anti-UCHL1 |
Enzo |
Cat# PG9500; RRID: AB_11181886 |
| Rat anti-Dopamine Transporter |
Millipore |
Cat# MAB369; RRID: AB_2190413 |
| Rat anti-LAMP1 |
Hybridoma Bank |
Cat# 1D4B; RRID: AB_2134500 |
| Rabbit anti-Clathrin [Clone D3C6] |
Cell Signaling |
Cat# 4796, RRID:AB_10828486 |
| Mouse anti-AP2α [Clone 3B5] |
ThermoFisher Scientific |
Cat# MA1-872, RRID:AB_2199412 |
| Rabbit anti-Arpc2 |
Novus Biological |
Cat# NBP1-88852, RRID:AB_11040464 |
| Mouse anti-APP |
Biolegend |
Cat# 802803, RRID:AB_2715853 |
| Mouse anti-PDH |
ThermoFisher Scientific |
Cat# 459400, RRID:AB_2532238 |
| Rabbit anti-Cathepsin D |
Abcam |
Cat# ab75852, RRID:AB_1523267 |
| Mouse anti-Hsc70 |
Novus Biological |
Cat# NB120-2788, RRID:AB_2120309 |
| Rat anti-Hsp90 |
Stressgen / Enzo Life sciences |
Cat# ADI-SPA-835-F, RRID:AB_11181205 |
| Rabbit anti-Hsp40 |
Stressgen / Enzo Life sciences |
Cat# ADI-SPA-400, RRID:AB_10631418 |
| Mouse anti-Rac1 |
Millipore |
Cat# 05-389, RRID:AB_309712 |
| Rabbit anti-Phlipp1 |
Bethyl |
Cat# A300-660A, RRID:AB_2283757 |
| Rabbit anti-Rictor |
Bethyl |
Cat# A300-459A, RRID:AB_2179967 |
| Rabbit anti-CathepsinA |
Abcam |
Cat#ab184553 |
| Rabbit anti-RARα |
Cell Signaling |
Cat# 2554, RRID:AB_2253585 |
| Mouse anti-CaMKIIα |
Millipore |
Cat# 05-532, RRID:AB_309787 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| Ammonium Chloride |
Sigma-Aldrich |
Cat #A9434 |
| B27 Supplement |
GIBCO-Invitrogen |
Cat# 17504044 |
| DMEM |
Sigma-Aldrich |
Cat# D5648 |
| Formaldehyde solution, 37wt |
Sigma-Aldrich (Merck) |
Cat#252549 |
| GlutaMAX |
ThermoFisher Scientific |
Cat# 35050-061 |
| Hoechst 33342 |
ThermoFisher Scientific |
Cat# H3570 |
| Leupeptin |
Sigma-Aldrich |
Cat# L5793 |
| Methanol |
Sigma-Aldrich (Merck) |
Cat#322415 |
| Neurobasal medium |
ThermoFisher Scientific |
Cat# 10888022 |
| Newborn Calf Serum |
Atlanta Biologicals |
Cat# S11250 |
| Oxyblot Protein Oxidation Detection Kit |
Merck-Millipore |
Cat# S7150 |
| Papain |
Sigma-Aldrich |
Cat# P3125 |
| Pierce ECL Western Blotting Substrate |
Thermo Fisher Scientific |
Cat#32106 |
| Prolong Diamond Antifade Mountant |
ThermoFisher Scientific |
Cat# P36961
|
| Sarkosyl |
Sigma-Aldrich |
Cat# L9150 |
| ThioflavineS |
Santa Cruz |
Cat#sc391005 |
| CyQuant |
ThermoFisher Scientific |
Cat#C7026 |
| Alexa555-conjugated Transferrin |
Life Technologies |
Cat# T35352
|
| Amyloid beta 42 Human ELISA |
ThermoFisher Scientific |
Cat # KHB3442 |
|
| Experimental models: cell lines |
|
|
|
| NIH 3T3 |
ATCC |
Cat# CRL-1658 |
| CAD |
ECACC |
Cat# 08100805, RRID:CVCL_0199 |
|
| Experimental models: organisms/strains |
|
|
|
| Mouse: B6.Cg-Tg(Camk2a-cre)T29-1Stl/J |
The Jackson Laboratory |
IMSR Cat# JAX:005359, RRID:IMSR_JAX:005359 |
| Mouse: B6.Cg-7630403G23RikTg(Th-cre)1Tmd/J |
The Jackson Laboratory, Savitt et al., 2005 |
IMSR Cat# JAX:008601, RRID:IMSR_JAX:008601 |
| Mouse: LAMP-2Aflox/flox
|
Schneider et al., 2014 |
N/A |
| Mouse: Atg7flox/flox
|
Komatsu et al., 2006 |
N/A |
| Mouse: Tg (APPSwe; PS2N141I; TauP301L) |
Grueninger et al., 2010 |
N/A |
| Mouse: TauP301L (line pR5) |
Kins et al., 2001 |
N/A |
| Mouse; TauP301S (line PS19) |
Yoshiyama et al., 2007 |
Cat# JAX:008169, RRID:IMSR_JAX:008169 |
|
| Software and algorithms |
|
|
|
| Adobe Photoshop 6.0 |
Adobe Systems |
https://www.adobe.com/ RRID:SCR_014199 |
| AxioVision Rel. 4.8 |
Carl Zeiss |
https://www.zeiss.com/ RRID:SCR_002677 |
| Cytoscape 3.7.1 |
|
Cytoscape, RRID: SCR_003032 |
| Enrichr |
Chen et al., 2013; Kuleshov et al., 2016
|
Enrichr, RRID:SCR_001575 |
| Fiji |
NIH |
https://fiji.sc/ RRID:SCR_002285 |
| Gene Set Enrichment Analysis |
Subramanian et al., 2005 |
Gene Set Enrichment Analysis, RRID:SCR_003199 |
| GraphPad Prism 8.0 |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/ RRID:SCR_002798 |
| KFERQ-finder |
Kirchner et al., 2019
https://doi.org/10.1371/journal.pbio.3000301
|
http://ec2-18-188-198-152.us-east-2.compute.amazonaws.com:3838/kferq/ |
| LAS AF Lite |
Leica |
https://www.leica-microsystems.com/ RRID:SCR_013673 |
| Matplotlib 3.1.1 |
Hunter et al., 2007 |
MatPlotLib, RRID: SCR_008624 |
| Numpy 1.17.2 |
van der Walt et al., 2011 |
NumPy, RRID: SCR_008633 |
| Python 3.7.4 |
Python Software Foundation |
Python Programming Language, RRID: SCR_008394 |
| SciPy 1.3.1 |
Jones et al., 2001 |
SciPy, RRID: SCR_008058 |
| ezTrack |
Pennigton et al., 2019 |
N/A |
| Seahorse Wase Desktop Software |
Agilent Techonologies |
Seahorse Wave, RRID:SCR_014526 |
|
| Other |
|
|
|
| Axiovert 200 with ApoTome 0.2 system fluorescence microscope |
Carl Zeiss, Albert Einstein College of Medicine |
https://www.zeiss.com/ |
| Fujifilm LAS-3000 Imager |
Fujifilm, Albert Einstein College of Medicine |
https://www.fujifilm.com/products/medical/ |
| Operetta system |
Perkin Elmer, Albert Einstein College of Medicine |
https://www.perkinelmer.com:443/product/operetta-cls-system-hh16000000 |
| Seahorse Biosciences Extracellular Flux Analyzer XFe24 |
Agilent, Albert Einstein College of Medicine |
https://www.agilent.com |
| SP8-LIA confocal microscope |
Leica Microsystems, Albert Einstein College of Medicine |
https://www.leica-microsystems.com/ |
