REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
α-Aβ	BioLegend	6E10; Cat#803001; RRID: AB_2564653
α-polyQ	Sigma Aldrich	3B5H10; Cat#MABN821; RRID: AB_532270
α-GFP/YFP	ChromoTek	3H9; Cat#3h9-100; RRID: AB_10773374
α-α-tubulin	Sigma Aldrich	B512; Cat#T5168; RRID: AB_477579
Bacterial and Virus Strains
E. coli OP50	CGC	WB OP50; RRID: WB-STRAIN:OP50
E. coli HT115	CGC	WB HT115; RRID: WB-STRAIN:HT115
L4440 RNAi	Addgene	Cat#1654
bec-1 RNAi	Vidal ORF-RNAi library, Source Bioscience	Cat#3320_Cel_ORF_RNAi
vps-34 RNAi	Vidal ORF-RNAi library, Source Bioscience	Cat#3320_Cel_ORF_RNAi
xbp-1 RNAi	Vidal ORF-RNAi library, Source Bioscience	Cat#3320_Cel_ORF_RNAi
asp-3 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
atg-13 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
atg-18 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
cup-5 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
hlh-30 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
lmp-1 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
vha-15 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
vha-18 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
vha-2 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
vha-8 RNAi	Ahringer library, Source Bioscience	Cat#3318_Cel_RNAi_complete
daf-2 RNAi	Dillin lab, UC Berkeley	N/A
daf-16 RNAi	Dillin lab, UC Berkeley	N/A
Chemicals, Peptides, and Recombinant Proteins
Carbenicillin	Formedium	Cat#CAR0025
IPTG	Generon	Cat#orb340528
Sodium azide	Sigma Aldrich	Cat#S2002
Levamisole	Sigma Aldrich	Cat#L0380000
Tetramisole	Sigma Aldrich	Cat#T1512-5G
Benzaldehyde	Sigma Aldrich	Cat#B1334-250ML
AlexaFluor 546-Phalloidin	Life Technologies Ltd.	Cat#A22283
Papain	AppliChem GmbH	Cat#A3824
Fetal bovine serum	GIBCO, Life Technologies	Cat#10270106
Trizol LS	Ambion, Life Technologies	Cat#10296010
SYBRGreen Master Mix	Applied Biosystems	Cat#4472897
cDCFDA	ThermoFisher	Cat#C369
LysoTracker DeepRed	ThermoFisher	Cat#L12492
Critical Commercial Assays
Pierce BCA protein assay kit	Thermo Scientific	Cat#23227
Direct-zol kit	Zymo Research	Cat#R2060
NuGEN Ovation RNaseq v2 kit	NuGEN	Cat#7102
Agilent High Sensitivity DNA kit	Agilent	Cat#5067-4626
Ovation Ultralow System v2 kit	NuGEN	Cat#0344
KAPA Library Quantification Kit	Illumina Platforms	Cat#07960140001
Agilent RNA 6000 Pico Kit	Agilent	Cat#5067-1513
QuantiTect reverse transcription kit	QIAGEN	Cat#205310
Fluorometric assay kit	Abcam	Cat#ab65300
Deposited Data
NCBI	BioProject	PRJNA482604
C. elegans strains
Wild type, Bristol	CGC [55]	N2
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]	CGC [6]	AGD927
dvIs50[snb-1::Aβ1-42, mtl-2::GFP]	CGC [13]	CL2355
dyn-1(ky51)	CGC [7]	CX51
let-60(ga89)	CGC [7]	SD551
rmIs132[unc-54p::Q35::YFP]	CGC [8]	AM140
dvIs2[unc-54p::Aβ1-42, rol-6(su1006)]	CGC [17]	CL2006
unc-15(e1402)	CGC [7]	CB1402
rde-1(ne219)	CGC [24]	WM27
rde-1(ne219); kbIs7 [nhx-2p::rde-1 + rol-6(su1006)]	CGC [25]	VP303
rde-1(ne219); jamSi2 [mex-5p::rde-1]	CGC [26]	AMJ345
pwIs50 [lmp-1p::lmp-1::GFP, Cbr-unc-119(+)])	CGC [29]	RT258
adIs2122[lgg-1p::GFP::lgg-1, rol-6(su1006)]	CGC [30]	DA2123
sqIs11[lgg-1p::mCherry::GFP::lgg-1+rol-6]	CGC [31]	MAH215
[sqIs17 [hlh-30p::hlh-30::GFP + rol-6]	CGC [27]	MAH240
rmIs110[rgef-1p::Q40::YFP]	Dillin lab (outcrossed from [14])	AGD1397
uthIs393[vha-6p::Q40::YFP, rol-6(su1006)]	Dillin lab (integrated from [19])	AGD1395
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]	This paper (integrated from [6])	AGD1379
uthIs390[unc-54p::xbp-1s, myo-2p::tdTomato]	This paper (integrated from [6])	AGD1391
zcIs18(ges-1p::GFP)	This paper (outcrossed from [22])	RCT51
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; dvIs2[unc-54p::Aβ1-42, rol-6(su1006)]	This paper	RCT1
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]; dvIs2[unc-54p::Aβ1-42, rol-6(su1006)]	This paper	RCT2
uthIs390[unc-54p::xbp-1s, myo-2p::tdTomato]; dvIs2[unc-54p::Aβ1-42, rol-6(su1006)]	This paper	RCT3
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; dvIs50[snb-1::Aβ1-42, mtl-2::GFP]	This paper	RCT23
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]; dvIs50[snb-1::Aβ1-42, mtl-2::GFP]	This paper	RCT25
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; rmIs132[unc-54p::Q35::YFP]	This paper	AGD1412
rmsEx15(gly-19p::xbp-1s, myo-2p::tdTomato); rmIs132[unc-54p::Q35::YFP]	This paper	RCT146
uthIs390[unc-54p::xbp-1s, myo-2p::tdTomato]; rmIs132[unc-54p::Q35::YFP]	This paper	RCT4
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; rmIs110[rgef-1p::Q40::YFP]	This paper	AGD1399
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]; rmIs110[rgef-1p::Q40::YFP]	This paper	RCT31
uthIs390[unc-54p::xbp-1s, myo-2p::tdTomato]; rmIs110[rgef-1p::Q40::YFP]	This paper	RCT32
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; uthIs393[vha-6p::Q40::YFP, rol-6(su1006)]	This paper	RCT33
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]; uthIs393[vha-6p::Q40::YFP, rol-6(su1006)]	This paper	RCT26
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; dyn-1(ky51)	This paper	RCT59
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; unc-15(e1402)	This paper	RCT60
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; let-60(ga89)	This paper	RCT112
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; zcIs18(ges-1p::GFP)	This paper	RCT52
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; rde-1(ne219); kbIs7 [nhx-2p::rde-1 + rol-6(su1006)]	This paper	RCT145
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT105
dvIs50[snb-1::Aβ1-42, mtl-2::GFP]; rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT109
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; dvIs50[snb-1::Aβ1-42, mtl-2::GFP]; rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT110
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]; dvIs50[snb-1::Aβ1-42, mtl-2::GFP]; rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT111
rmIs110[rgef-1p::Q40::YFP]); rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT106
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; rmIs110[rgef-1p::Q40::YFP]); rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT107
uthIs388[gly-19p::xbp-1s, myo-2p::tdTomato]; rmIs110[rgef-1p::Q40::YFP]); rde-1(ne219); jamSi2 [mex-5p::rde-1]	This paper	RCT108
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; sqIs17 [hlh-30p::hlh-30::GFP + rol-6]	This paper	RCT94
uthIs270 [rab-3p::xbp-1s, myo-2p::tdTomato]; pwIs50 [lmp-1p::lmp-1::GFP, Cbr-unc-119(+)]	This paper	RCT103
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; adIs2122[lgg-1p::GFP::lgg-1, rol-6(su1006)]	This paper	RCT104
uthIs270[rab-3p::xbp-1s, myo-2p::tdTomato]; sqIs11[lgg-1p::mCherry::GFP::lgg-1+ rol-6]	This paper	RCT98
Oligonucleotides
See Table S2	N/A	N/A
Software and Algorithms
SeqMonk	Babraham Institute	https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
g:Profiler	ELIXIR	https://biit.cs.ut.ee/gprofiler/index.cgi
Promoterome Database	Harvard University	http://worfdb.dfci.harvard.edu/promoteromedb/