REAGENT OR RESOURCE	SOURCE	IDENTIFIER
Antibodies
Active-Caspase3 (rabbit)	R&D Systems	Cat#AF835, RRID:AB_2243952
ATG5 (rabbit)	LifeSpan BioSciences Inc.	LS-C156610
Calnexin (rabbit)	Abcam	Cat#ab75801, RRID:AB_1310022
Calreticulin (rabbit)	Thermo Fisher Scientific	Cat# PA3-900, RRID:AB_325990
Cav2.1 (rabbit)	Synaptic Systems	Cat# 152 203, RRID:AB_2619841
CytochromeC (mouse)	BD Biosciences	Cat# 556433, RRID:AB_396417
DHRP (mouse)	Abcam	Cat# ab2864, RRID:AB_303365
FK2(ubi) (mouse)	Enzo Life Sciences	Cat# BML-PW8810 0500, RRID:AB_2051891
GAD65 (guinea pig)	Synaptic Systems	Cat# 198104, RRID:AB_10557995
GFAP (mouse)	Sigma-Aldrich	Cat# G3893, RRID:AB_477010
GluA1 (rabbit)	Millipore	Cat# ABN241, RRID:AB_2721164
GluN1 (mouse)	Synaptic Systems	Cat# 114 011, RRID:AB_887750
GM130 (mouse)	BD Biosciences	Cat# 610822, RRID:AB_10015242
Homer1 (rabbit)	Synaptic Systems	Cat# 160 003, RRID:AB_887730
HSC70 (rabbit)	Abcam	Cat# ab51052, RRID:AB_880538
IP3R1 (rabbit)	Cell Signaling Technology	Cat# 8568, RRID:AB_10890699
IP3R3 (rabbit)	Millipore	Cat# AB9076, RRID:AB_11212608
Kv pan (mouse)	UC Davis/NIH NeuroMab Facility	Cat# 75-392, RRID:AB_2491089
Kv1.1 (mouse)	UC Davis/NIH NeuroMab Facility	Cat# 75-007, RRID:AB_10673165
Kv1.2 (mouse)	UC Davis/NIH NeuroMab Facility	Cat# 75-008, RRID:AB_2296313
Kv1.4 (rabbit)	Novus Biologicals	NBP2-75552
Lamp1 (rat)	BD Biosciences	Cat# 553792, RRID:AB_2134499
LC3 (mouse)	MBL International	Cat# M152-3, RRID:AB_1279144
LC3B (rabbit)	Novus	Cat# NB600-1384, RRID:AB_669581
Map2 (mouse)	Sigma-Aldrich	Cat# M9942, RRID:AB_477256
Map2 (guinea pig)	Synaptic Systems	Cat# 188 004, RRID:AB_2138181
Munc13-1 (guinea pig)	Synaptic Systems	Cat# 126 104, RRID:AB_2619806
NaV pan (rabbit)	Gentex	GTX16935
P62 (guinea pig)	Progen	Cat# GP62-C, RRID:AB_2687531
PI(4)P (mouse)	Echelon Biosciences	at# Z-P004, RRID:AB_11127796
PI(4,5P2) (mouse)	Echelon Biosciences	Cat# Z-A045, RRID:AB_427211
Piccolo (rabbit)	Synaptic Systems	Cat# 142 002, RRID:AB_887759
PMCA (mouse)	Thermo Fisher Scientific	Cat# MA3-914, RRID:AB_2061566
PSD95 (guinea pig)	Synaptic Systems	Cat# 124 014, RRID:AB_2619800
Reticulocalbin 2 (rabbit)	Atlas Antibodies	Cat# HPA030694, RRID:AB_2673573
Reticulon 3 (rabbit)	Millipore	ABN 1723
RYR pan (mouse)	Enzo Life Sciences	Cat# ALX-804-016-R100, RRID:AB_2052517
RYR2 (guinea pig)	Frontier Institute	RyR2-GP-Af480
RyR2 (rabbit)	Millipore	Cat# AB9080, RRID:AB_11211327
Sec6b and anti-Sec61a (rabbit)	Tom Rapoport	N/A
Serca2 (mouse)	Thermo Fisher Scientific	Cat# MA3-919, RRID:AB_325502)
SNAP25 (mouse)	Synaptic Systems	Cat# 111 011, RRID:AB_887794
Sod2 (rabbit)	Abcam	at# ab13498, RRID:AB_300402
SV2A (mouse)	Pietro De Camilli	N/A
Synapsin (mouse)	Synaptic Systems	Cat# 106 001, RRID:AB_887805
Synaptobrevin 2 (guinea pig)	Synaptic Systems	Cat# 104 204, RRID:AB_2212601
Synaptotagmin1 (mouse)	Synaptic Systems	Cat# 105 011C5, RRID:AB_2619761
Synaptotagmin1 (luminal)-Cy3 (rabbit)	Synaptic Systems	Cat# 105 103C3 RRID:AB_887829
Tau1 (mouse)	Millipore	Cat# MAB3420, RRID:AB_11213630
Tubb3 (rabbit)	Synaptic Systems	Cat# 302 302, RRID:AB_10637424
Tubulin (mouse)	Sigma-Aldrich	Cat# T5168, RRID:AB_477579
VapB (rabbit)	Abnova Corporation	Cat# H00009217-D01, RRID:AB_10720965
VGAT (rabbit)	Synaptic Systems	Cat# 131 003, RRID:AB_887869
VGLUT (guinea pig)	Synaptic Systems	Cat# 135 304, RRID:AB_887878
Vinculin (mouse)	Sigma-Aldrich	Cat# V9264, RRID:AB_10603627
Goat anti mouse IgG Alexa Fluor 568	Thermo Fisher Scientific	Cat# A-11031 RRID: AB_144696
Goat anti mouse IgG Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11001; RRID: AB_2534069
Goat anti rabbit IgG Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11008; RRID: AB_143165
Goat anti rabbit IgG Alexa Fluor 568	Thermo Fisher Scientific	Cat# A-11011; RRID: AB_143157
Donkey anti rat IgG Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-21208, RRID:AB_2535794
Goat anti guinea pig IgG Alexa Fluor 568	Thermo Fisher Scientific	Cat# A-11075, RRID:AB_2534119
Goat anti guinea pig IgG Alexa Fluor 647	Thermo Fisher Scientific	Cat# A-21450, RRID:AB_2735091
IRDye® 800CW Goat Anti-Mouse IgG	LI-COR Biosciences	Cat# 926-32210, RRID:AB_621842
IRDye® 680RD Goat anti-Mouse IgG	LI-COR Biosciences	Cat# 925-68070, RRID:AB_2651128
IRDye 680RD Goat anti-Rabbit IgG	LI-COR Biosciences	Cat# 926-68071, RRID:AB_10956166
IRDye® 800CW Goat Anti-Rabbit IgG,	LI-COR Biosciences	Cat# 926-32211, RRID:AB_621843
IRDye 680RD Donkey anti-Guinea pig IgG	LI-COR Biosciences	Cat# 926-68077, RRID:AB_10956079
IRDye® 800CW Donkey Anti- Guinea pig IgG	LI-COR Biosciences	Cat# 926-32411, RRID:AB_1850024
Bacterial and Virus Strains
Lenti f(U6)sNLS-RFPw	Viral core facility of the Charité – Universitätsmedizin Berlin, Germany	Cat#BLV-360 https://vcf.charite.de/en/
Lenti f(syn)-Syp-GCamp6f-w	Viral core facility of the Charité – Universitätsmedizin Berlin, Germany	Cat#BLV-700 https://vcf.charite.de/en/
Chemicals, Peptides, and Recombinant Proteins
Picrotoxin	Sigma-Aldrich	Cat#P1675
Tamoxifen ((Z)-4-Hydroxytamoxifen)	Sigma-Aldrich	Cat# H7904
Thapsigargin	Sigma-Aldrich	Cat# T9033
Dantrolene	Sigma-Aldrich	Cat# 251680
Ionomycin	Sigma-Aldrich	Cat# 407952
Bafilomycin A1	Enzo	Cat# BML-CM110-0100
Caffein	Sigma-Aldrich	Cat# c0750
Doxycycline hyclate	Sigma-Aldrich	Cat#D9891
D4-lysine	Silantes	Cat#211104113
13C6-arginine	Silantes	Cat#201204102
13C615N2-lysine	Silantes	Cat#211603902
13C615N4-arginine	Silantes	Cat#201603902
Critical Commercial Assays
ProFection Mammalian Transfection System – Calcium Phosphate	Promega	Cat# E1200
Fluo-8H	AAT Bioquest	Cat# 21080
Experimental Models: Organisms/Strains
Mouse: C57BL/6J	Charles River	RRID: IMSR_JAX:000664
Mouse: B6.129S-Atg5tm1Myok	RIKEN BioResource Center	Cat# RBRC02975, RRID:IMSR_RBRC02975
Mouse: BC.Cg-Tg(CAG-cre/Esr1∗)5Amc/J	The Jackson Laboratory	Cat# JAX:004682, RRID:IMSR_JAX:004682
Mouse: Emx1-Cre	RIKEN BioResource Center	Cat# RBRC01342, RRID:IMSR_RBRC01342
Oligonucleotides
See Table S2		N/A
Recombinant DNA
Synaptophysin -pHluorin	L. Lagnado	N/A
sRed2-Mito-7	Michael Davidson	RRID:Addgene_55838
TetOn-eGFP-mCherry-RAMP4	Liang et al., 2018	RRID:Addgene_109014
TOM20MTS-mCherry-EGFP-Tet-On	Liang et al., 2018	RRID:Addgene_09016
pEGFP-LC3	Lee et al., 2008	RRID:Addgene_24920
mRFP-LC3	Kimura et al., 2007	RRID:Addgene_ 21075
ER-GCAMP6-150	de Juan-Sanz et al., 2017	RRID:Addgene_ 86918
GCamp6f	Chen et al., 2013	RRID:Addgene_40755
Software and Algorithms
Prism 5	Graph Pad	RRID: SCR_002798
Fiji (ImageJ)	NIH	RRID: SCR_002285
MaxQuant software	MaxQuant	RRID:SCR_014485
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool	Eden et al., 2009	RRID:SCR_006848
Etomo/IMOD	Kremer et al., 1996	https://bio3d.colorado.edu/imod/
Microscopy imaging browser MIB	Belevich et al., 2016	http://mib.helsinki.fi/index.html
BLOCK-iT RNAi Designer	Thermo Fisher Scientific	RRID:SCR_002794
Biosettia shRNA design	Biosettia	N/A
Image Studio Lite	LI-COR Biosciences	RRID:SCR_013715
SigmaPlot	Systat Software, Inc.	RRID:SCR_003210
IGOR Pro	WaveMetrics, Lake Oswego, OR	RRID:SCR_000325
PatchMaster software	Heka Elektronics	RRID:SCR_000034