Table 2 Detailed information on the 30 primary antibodies used

Disease-related markers

Alzheimer’s disease (AD) tangle

Phospho-Tau Ser202, Thr205, clone AT8

ms

1:200

Thermo Fisher Scientific Cat# MN1020, RRID:AB_223647

Immunogen based on human sequence, reacts with human

AD plaque

β-Amyloid, 17–24, clone 4G8

ms

1:1000

BioLegend Cat# 800701, RRID:AB_2564633

Immunogen based on human sequence, reacts with human

Neuronal cells

 A1

Pyramidal neuron

CAMKIIA (CAMK2A)

rb

1:300

Abcam Cat# ab103840, RRID:AB_10900968

Immunogen based on human sequence

 A2

Purkinje cell

Calbindin D28k (CALB1)

rb

1:300

Synaptic Systems (SySy) Cat# 214 003, RRID:AB_2619901

Immunogen based on human sequence, reacts with human

 A3

Purkinje cell

CALB1

ms

1:300

SySy Cat# 214 011, RRID:AB_2068201

Immunogen based on human sequence, reacts with human

 A4

Interneuron

CRH

ms

1:100

Sigma-Aldrich Cat# WH0001392M2, RRID:AB_1840911

Immunogen based on human sequence, reacts with human

 A5

Catecholaminergic neuron

TH

ms

1:200

Millipore Cat# MAB318, RRID:AB_2201528

Reacts with human

Glial cells

 B

Microglia

IBA1 (AIF1)

rb

1:200

SySy Cat# 234 003, RRID:AB_10641962

Reacts with human, K.O. verified (SySy)

 C1

Astrocyte

GFAP

rb

1:250

Agilent Cat# Z0334, RRID:AB_10013382

Reacts with human

 C2

Astrocyte

GFAP

ms

1:200

SySy Cat# 173 011, RRID:AB_2232308

Immunogen based on human sequence, reacts with human, K.O. verified (SySy)

 C3

Astrocyte (mature)

S100B

gp

1:200

SySy Cat# 287 004, RRID:AB_2620025

 D1

Oligodendrocyte (myelin sheath)

MBP

rb

1:200

Abcam Cat# ab133620, no RRID available

Immunogen based on human sequence, reacts with human

 D2

Oligodendrocyte (myelin sheath)

MBP, clone SMI 94

ms

1:200

BioLegend Cat# 836504, RRID:AB_2616694

Immunogen based on human sequence, reacts with human

 D3

Oligodendrocyte (myelin sheath)

MBP

ms

1:100

Atlas Antibodies Cat# AMAb91064, RRID:AB_2665784

Immunogen based on human sequence, reacts with human

Neuronal compartments

Neuronal processes

 E1

Axon

Pan-axonal neurofilament, clone SMI-312

ms

1:200

BioLegend Cat# 837904, RRID:AB_2566782

Reacts with human

 E2

Axon, paranodal region

Caspr/paranodin (CNTNAP1)

ms

1:100

UC Davis/NIH NeuroMab Facility Cat# 75–001, RRID:AB_2083496

Reacts with human

 F

Dendrite

MAP2

ms

1:200

Millipore Cat# MAB3418, RRID:AB_94856

Reacts with human

Synaptic proteins & organelles

 G1

Presynapse (synaptic vesicle)

Synapsin 1/2

rb

1:200

SySy Cat# 106 003, RRID:AB_2619773

Reacts with human, K.O. verified (SySy)

 G2

Presynapse (synaptic vesicle)

Synaptophysin 1 (SYP)

gp

1:500

SySy Cat# 101 004, RRID:AB_1210382

Immunogen based on human sequence, reacts with human

 G3

Presynapse (synaptic vesicle)

SYP

rb

1:100

Abcam Cat# ab14692, RRID:AB_301417

Immunogen based on human sequence

 G4

Presynapse (GABAergic synaptic vesicle)

VGAT, cytoplasmic domain (SLC32A1)

ms

1:50

SySy Cat# 131 011, RRID:AB_887872

Reacts with human, K.O. verified (SySy)

 G5

Presynapse (glutamatergic synaptic vesicle)

VGLUT1 (SLC17A7)

gp

1:200

SySy Cat# 135 304, RRID:AB_887878

Reacts with human, K.O. verified (SySy)

 G6

Postsynapse (inhibitory)

Gephyrin (GPHN)

ms

1:100

SySy Cat# 147 011, RRID:AB_887717

Reacts with human, K.O. verified (SySy)

 G7

Postsynapse (excitatory)

GLUA2 (GRIA2)

ms

1:200

SySy Cat# 182 111, RRID:AB_10645888

 G8

Postsynapse (excitatory)

HOMER3

rb

1:300

SySy Cat# 160 303, RRID:AB_10804288

 G9

Postsynapse (excitatory)

PSD-95, PDZ domain (DLG4)

ms

1:100

SySy Cat# 124 011, RRID:AB_10804286

K.O. verified (SySy)

 H

Endoplasmic reticulum

Calreticulin (CALR)

rb

1:200

SySy Cat# 315 003, RRID:AB_2620050

Others

 J1

Basal lamina (e.g., in vessels)

Collagen IV

ms

1:200

Agilent Cat# M0785, RRID:AB_2082944

Immunogen based on human sequence, reacts with human

 J2

Smooth muscle cell (e.g., in vessels)

α-Actin (smooth muscle)

ms

1:200

Agilent Cat# M0851, RRID:AB_2223500

Immunogen based on human sequence, reacts with human

 K

Cells using glycolysis

GAPDH

rb

1:100

SySy Cat# 247 002, RRID:AB_10804053

Immunogen based on human sequence, reacts with human