REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Cyclin A	Santa Cruz Biotechnology	Cat# sc-751; RRID:AB_631329
P19 Arf	Novus Biologicals	Cat# NB200-169
p21 Cip1	Millipore	Cat# MAB88058; RRID:AB_11212534
p27 Kip1	Millipore	Cat# 06-445; RRID:AB_310121
p27 Kip ( Clone DCS-72.F6)	ThermoFisher	Cat# MS-256-P0
p27Kip (F8)	Santa Cruz Biotechnology	Cat# sc-1641; RRID:AB_628074
NFkB p65	Cell Signaling Technology	Cat# 4764; RRID:AB_823578
phospho-NF-kB p65 (Ser365) (93H1)	Cell Signaling Technology	Cat# 3033; RRID:AB_331284
Cyclin A	Santa Cruz Biotechnology	Cat# sc-751; RRID:AB_631329
P19 Arf	Novus Biologicals	Cat# NB200-169
Ki67	Novo CASTRA	Cat# NCL-Ki67p
Ki67	eBioscience	Cat# 14-5698
Phospho-p53 (Ser15)	Abcam	Cat# ab1431; RRID:AB_301090
Phospho-p53 (Ser15) (D4S1H)	Cell Signaling Technology	Cat# 12571; RRID:AB_2714036
Phospho-p53 (Ser15) (16G8)	Cell Signaling Technology	Cat# 9286; RRID:AB_331741
Phospho-ATM(Ser1981)	Novus Biologicals	Cat# AF1655
Phospho-ATR (Ser 428)	Cell Signaling Technology	Cat# 2853; RRID:AB_2290281
53 BP1	Novus Biologicals	Cat# NB100-304
Brca1	Santa Cruz Biotechnology	Cat# sc-642; RRID:AB_630944
Brca1	Novus Biologicals	Cat# MAB22101
Brca1 (clone 8F7)	Novus Biologicals	Cat# NBP1-41186
LC3B (G-9)	Santa Cruz Biotechnology	Cat# sc-376404; RRID:AB_11150489
LC3B	Cell Signaling Technology	Cat# 2775; RRID:AB_915950
LC3B	Novus Biologicals	Cat# NB100-2220
p62SQSTM1	Novus Biologicals	Cat# MAB8028
p62SQSTM1	GeneTex	Cat# GTX100685; RRID:AB_2038029
Fibronectin	BD Biosciences	Cat# 610077; RRID:AB_2105706
Phospho-Tau (Thr181) 5H9L11	Thermo Fisher	Cat# 701530; RRID:AB_2532491
Phospho-Tau (Ser202/Thr205) mAb (AT8)	ThermoFisher	Cat# MN1020; RRID:AB_223647
Phospho-Tau (Thr231)	ThermoFisher	Cat# 44-746G; RRID:AB_2533742
Phospho-Tau (Ser416) D7U2P	Cell Signaling Technology	Cat# 15013; RRID:AB_2728782
Phospho-Tau (Thr 217)	GenScript	Cat# A00896; RRID:AB_2622113
Phospho-Tau (Ser396)	GenScript	Cat# A01387; RRID:AB_1575880
Tau (Tau 46)	Santa Cruz Biotechnology	Cat# sc32274; RRID:AB_628327
Tau (A10)	Santa Cruz Biotechnology	Cat# sc-390476
Tau (TAU-5)	Santa Cruz Biotechnology	Cat# sc-58860; RRID:AB_785931
Prp (6D11)	Santa Cruz Biotechnology	Cat# sc-58581; RRID:AB_1128724
Histone H1.0	Active Motif	Cat# 61417; RRID:AB_2793627
Histone H1	Active Motif	Cat# 39707; RRID:AB_2793314
Histone H1 (AE-4)	Santa Cruz Biotechnology	Cat# sc-8030; RRID:AB_675641
Histone H2A (D6O3A) Rabbit mAb	Cell Signaling Technology	Cat# 12349; RRID:AB_2687875
Histone H2A II	Cell Signaling Technology	Cat# 2578; RRID:AB_2118804
Histone H2A, Clone C10037	MBL	Cat# D210-3
Histone H2A C-terminal antibody (pAb)	Active Motif	Cat# 39591; RRID:AB_2793270
Histone H2A	GeneTex	Cat# GTX129418; RRID:AB_2885986
Ubiquityl-Histone H2AK119	Cell Signaling Technology	Cat# 8240; RRID:AB_10891618
Ubiquityl-Histone H2A Clone E6C5	Millipore	Cat# 05-678; RRID:AB_11214408
Histone H2A.X	Active Motif	Cat# 39689; RRID:AB_2728764
Histone H2A.Z	Cell Signaling Technology	Cat# 2718; RRID:AB_659840
phospho-Histone H2A.X (Ser139), clone JBW301	Millipore	Cat# 05-636; RRID:AB_309864
phospho-Histone H2A.X (Ser139)	Cell Signaling Technology	Cat# 2577; RRID:AB_2118010
phapho-Histone H2A.X (Ser139)	Active Motif	Cat# 39117; RRID:AB_2793161
phospho-Histone H2A.X (Ser139)	Bethyl Laboratories	Cat# IHC-00059-3
phospho-Histone H2A.X (Ser139) Clone 2F3	Biolegend	Cat# 613401; RRID:AB_315794
H2A.Y/macroH2A.1	Cell Signaling Technology	Cat# 8551; RRID:AB_2797647
H2A.Y/macroH2A.1 Clone 866416	Novus Biologicals	Cat# MAB8318
Histone H2B	Active Motif	Cat# 39125; RRID:AB_2793163
Ubiquityl-Histone H2B K120	Active Motif	Cat# 39623; RRID:AB_2793279
Histone H3	Active Motif	Cat# 61799; RRID:AB_2793771
Histone H3K9me3	Abcam	Cat# ab8898; RRID:AB_306848
Histone H3 (1G1)	Epigentek	Cat# A68386
Histone H3	Cell Signaling Technology	Cat# 9715; RRID:AB_331563
Histone H3.3	Novus Biologicals	Cat# NBP2-24697
Histone H4	Active Motif	Cat# 39269; RRID:AB_2636967
Histone H4	GeneTex	Cat# GTX129560; RRID:AB_2886030
Lamin B1	Abcam	Cat# ab16048; RRID:AB_443298
Lamin B1 (M20)	Santa Cruz Biotechnology	Cat# sc-6217; RRID:AB_648158
Lamin A/C	Cell Signaling Technology	Cat# 4777; RRID:AB_10545756
Lamin A/C	BD Biosciences	Cat# 612162; RRID:AB_399533
Ring1B (D22F2)	Cell Signaling Technology	Cat# 5694; RRID:AB_10705604
RNF168	Santa Cruz Biotechnology	Cat# sc-101125
RNF168	Millipore	Cat# ABE367; RRID:AB_11205761
MMP1	GeneTex	Cat# GTX100534S; RRID:AB_10724220
MMP2	GeneTex	Cat# GTX104577; RRID:AB_1950932
MMP2	Proteintech	Cat# 66366-1; RRID:AB_2881746
OPN	Novus Biologicals	Cat# AF808
Pai1	Proteintech	Cat# 13801-1-AP; RRID:AB_2186881
CD68 (KP1)	Abcam	Cat# ab955; RRID:AB_307338
CD68 (FA-11)	Abcam	Cat# ab53444; RRID:AB_869007
Iba	Wako	Cat# 019-19741; RRID:AB_839504
GFAP	Abcam	Cat# ab7260; RRID:AB_305808
GFAP	Dako	Cat# GA52461-2
GFAP (GA5)	Novus Biologicals	Cat# NBP2-29415
NeuN	Cell Signaling Technology	Cat# 24307; RRID:AB_2651140
NeuN, Clone A60	Millipore	Cat# MAB377; RRID:AB_2298772
Cleaved Caspase-3	Cell Signaling Technology	Cat# 9661; RRID:AB_2341188
Cleaved Caspase-3	Cell Signaling Technology	Cat# 9664; RRID:AB_2070042
Ubiquitin, Clone Ubi-1	Millipore	Cat# MAB1510; RRID:AB_2180556
Ubiquitin (Ubi-1)	Novus Biologicals	Cat# NB300-130
Ubiquitin	Millipore	Cat# AB1690; RRID:AB_2180744
Multiubiquitin Chain, Clone FK1	Cayman Chemical	Cat# 14219
Multiubiquitin Chain, Clone FK2	Cayman Chemical	Cat# 14220
Ubiqutin K48 linkage specific	Millipore	Cat# 05-1307; RRID:AB_1587578
Ubiqutin K63 linkage specific	Millipore	Cat# 05-1313; RRID:AB_1587585
Ubiqutin K11 linkage	Millipore	Cat# MABS107-I; RRID:AB_2713901
20S Proteasome alpha 2 (B4)	Santa Cruz Biotechnology	Cat# sc-377148
20S Proteasome beta 2 (D8)	Santa Cruz Biotechnology	Cat# sc-515066
Nucleoporin p62	BD Biosciences	Cat# 610497; RRID:AB_397863
Smc1	Novus Biologicals	Cat# NB100-204
GAPDH	Sigma	Cat# G9295; RRID:AB_1078992
Actin	Sigma	Cat# A2668; RRID:AB_258014
Tubulin, alpha, clone B-5-1-2	Sigma	Cat# T6074; RRID:AB_477582
Vinculin	Sigma	Cat# V9131; RRID:AB_477629
Biological samples
Human postmortem cerebral cortical tissue samples		See Table S3: Human Postmortem AD and Control Brain Tissue Specimen Table.
Chemicals, peptides, and recombinant proteins
Formaldehyde, EM grade	Ted Pella	Cat# 18505
Glutaraldehyde, EM grade	Ted Pella	Cat# 18421
X-Gal	ThermoFisher	Cat# R0404
N-Ethylmaleimide	Pierce	Cat# 23030
Iodoacetamide	Sigma	Cat# I1149
TRIzol Reagent	Invitrogen	Cat# 15596018
Leupeptin	ThermoFisher	Cat# 78435
Pepstatin A	ThermoFisher	Cat# 78436
Aprotinin	Sigma	Cat# A6103
Benzamidine	Sigma	Cat# 434760
Phenylmethanesulfonyl fluoride	Sigma	Cat# P7626
cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail	Roche	Cat# 11836170001
Chloroquine	Sigma	Cat# C6628
MG-132	selleckchem	Cat# S2619
FD Rapid GolgiStain kit	FD NeuroTechnologies	Cat# PK401
Antigen unmasking solution	Vector Lab	Cat# H-3300
DAB substrate Kit	Vector Lab	Cat# SK-4100
Critical commercial assays
20S Proteasome Assay Kit	Millipore	Cat # APT280
FD Rapid GolgiStain kit	FD Neuro Technologies	Cat # PK401
Deposited data
RNA-Seq Data	GEO	GSE183383
Experimental models: Organisms/strains
Brap knockout mice	generated in house (Lanctot et al., 2013)	https://www.sciencedirect.com/science/article/pii/S1534580713002177
Brap floxed mice	generated in house (Lanctot et al., 2017)	https://www.sciencedirect.com/science/article/pii/S2211124717309713?via%3Dihub
Emx1-Cre mice	JaxMice	Cat# 005628
Thy1-Cre mice	JaxMice	Cat# 006143
Oligonucleotides
qPCR primers	IDT	See Table S4 for a list of sequences of qRT-PCR primers
Software and algorithms
Image-Pro Premier	Media Cybernetics	https://www.mediacy.com/support/imagepropremier
Image J	ImageJ	https://imagej.nih.gov/ij/
GraphPad Prism	GraphPad	https://www.graphpad.com/scientific-software/prism/