REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, Peptides, and Recombinant Proteins
BsmAI	New England Bioloabs	R0529
Mouth aspirator and Microcapillary tubes	Sigma	P0674
Levamisole hydrochloride	Sigma	L0380000
Trizol Reagent	Life Technologies	15596026
Pronase	Sigma	10165921001
30 μm filters	Sysmex	SYS-04-004-2326
Trizol LS Reagent	Life technologies	10296028
DTT	Sigma	10197777001
MiRneasy column RNA kit	QIAGEN	217004
Phenol Chloroform Isoamyl	Sigma	P2069
Heavy Phase Lock tube	QuantaBio	23028330
RNA 5′ Polyphosphatase	Epicenter	RP8092H
NEBNext® Multiplex Small RNA Library Prep Set for Illumina	New England Biolabs	E7300
TruSeq Small RNA Library Prep Kit	Illumina	RS-200-0012
TapeStation screen tapes	Agilent	5067-5582 5067-5588
TapeStation reagents	Agilent	5067-5583 5067-5589
E-Gel 4% agarose	Life Technologies	G401004
MinElute DNA purification kit	QIAGEN	28006
SMART-Seq v4 Ultra Low Input RNA Kit	Nextera	634890
Nextera XT DNA Library Preparation Kit	Illumina	FC-131-1024
10X Phosphate Buffered Saline (PBS)	Ambion	AM9624
Formaldehyde	Sigma	F8775
RNase free Nuclease-free water	Ambion	AM9932
Dextran sulfate	Sigma	D8906-50G
Escherichia coli tRNA	ROCHE	10109541001
Vanadyl ribonucleoside complex	New England Biolabs	S1402S
RNase free BSA	Ambion	AM2618
Formamide	Ambion	AM9342
20X SSC	Ambion	AM9763
1 M Tris-HCl, pH 8.0	Ambion	AM9855G
Glucose oxidase stock	Sigma	G2133
Catalase suspension	Sigma	C3515
DAPI	Sigma	D9542
Sodium Azide	Sigma	S2002
Isoamyl alcohol	Sigma	W205702
Benzaldehyde	Sigma	418099
Diacetyl	Sigma	8.03528
Butanone	Sigma	360473
polydimethylsiloxane (PDMS)	Dow Corning Sylgard	4019862
Milltex 1 mm biopsy punchers	Fisher	12-460-401
PTFE microbore tubing	Cole-Parmer	EW-06417-21
Critical Commercial Assays
Affymetrix GeneChip® C. elegans Genome Array oligonucleotide arrays	Thermo Fisher	900383
Deposited Data
Small RNA-seq data	This study	GEO: GSE124049
Experimental Models: Organisms/Strains
wild type Bristol isolate	CGC	N2
rde-4(ne299)	Hobert lab	N/A
otIs356[rab-3p(prom1)::2xNLS::TagRFP]	Oren-Suissa lab	OH10690
sid-1(qt9)	CGC	HC196
ttTi5605 II; unc-119(ed3) III; oxEx1578	CGC	EG6699
rde-4(ne299) (6X outcrossed)	This study	BFF12
sid-1(qt9); rde-4(ne299)	This study	BFF13
rde-4(ne299); pigEx9[Psng-1::rde-4:SL2:yfp+Pmyo-3::Mcherry]	This study	BFF14
rde-4(ne299); pigEx10[Prgef-1::rde-4:SL2:yfp+Punc-122::gfp]	This study	BFF15
rde-4(ne299);pigSi3[cb-unc-119(+)Psng-1::rde-4:SL2:yfp]	This study	BFF16
rde-4(ne299); hrde-1(pig4)	This study	BFF17
rde-4(ne299); hrde-1(pig4); pigEx9[Psng-1::rde-4:SL2:yfp+Pmyo-3::Mcherry]	This study	BFF18
rde-4(ne299); sid-1(qt9); pigEx9[Psng-1::rde-4:SL2:yfp+Pmyo-3::Mcherry]	This study	BFF19
unc-119(ed3) III, oxTi38[cb-unc-119(+)Ppie-1::GFP]	Gift from Christian Frøkjær-Jensen	EG6089
hrde-1(tm1200); EG6089	This study	BFF20
rde-4(ne299); EG6089	This study	BFF21
rde-4(ne299); hrde-1(pig4); EG6089	This study	BFF22
otIs356[rab-3p(prom1)::2xNLS::TagRFP] (3x outcrossed)	This study	BFF30
rde-4(ne299); otIs356[rab-3p(prom1)::2xNLS::TagRFP]	This study	BFF31
rde-4(ne299); pigSi3[cb-unc-119(+)Psng-1::rde-4:SL2:yfp]; otIs356[rab-3p(prom1)::2xNLS::TagRFP].	This study	BFF32
sid-1(qt9); rde-4(ne299); pigSi3[cb-unc-119(+)Psng-1::rde-4:SL2:yfp];	This study	BFF33
hrde-1(pig4); rde-4(ne299); pigSi3[cb-unc-119(+)Psng-1::rde-4:SL2:yfp)]	This study	BFF34
kyEx2373[Pstr-2::Gcamp; Punc-122:GFP]	Hendricks lab	CX10281
rde-4(ne299); kyEx2373 [Pstr-2::Gcamp; Punc-122:GFP]	This study	BFF35
rde-4(ne299); saeg-2(syb776)	SunyBiotech	PHX776
rde-4(ne299); saeg-2(syb777)	SunyBiotech	PHX777
rde-4(ne299); saeg-2(syb776) (x2 outcrossed to rde-4)	This study	BFF36
rde-4(ne299); saeg-2(syb777) (x2 outcrossed to rde-4)	This study	BFF37
rde-4(ne299); saeg-2(pig5)	This study	BFF38
rrf-1(ok589)	CGC	RB798
dcr-1(mg375)	CGC	YY470
ergo-1 (tm1860)	CGC	WM158
rrf-3(pk1426)	CGC	NL2099
mut-16(pk710)	CGC	NL1810
eri-6(mg379)	CGC	GR181
nrde-3 (gg66)	CGC	YY158
Recombinant DNA
pos-1 RNAi plasmid	Vidal RNAi library	N/A
mel-26 RNAi plasmid	Vidal RNAi library	N/A
GFP RNAi plasmid	Hekimi lab- McGill	N/A
Oligonucleotides
PCR 1-FWD: genomic DNA rde-4 ATGGATTTAACCAAACTAACGTTTG	IDT	N/A
PCR 1-RV: genomic DNA rde-4 TCAATCCGTGAAATCATAGGTGTTG	IDT	N/A
PCR 2-FWD: Psng-1 AAACTGCAGTTAATTGTTAATTATCTAAGCTTG	IDT	N/A
PCR 2-RV: Psng-1 CGGGATCCGCTAAAATAAAAGAAATATAGAGG	IDT	N/A
PCR 3-FWD: Prgef-1 AAACTGCAGGCAGAATCGAGTCAACTGAAATCCG	IDT	N/A
PCR 3-RV: Prgef-1 AAAGGATCCCGTCGTCGTCGTCGATGC	IDT	N/A
PCR 4-FWD: hrde-1 (pig4) TCCACGTCCAATCCTTTGAGTG	IDT	N/A
PCR 4-RV: hrde-1 (pig4) AAGTTGCCCAGGGGGGT	IDT	N/A
PCR 5-FWD: saeg-2 (pig5) / saeg-2 (syb776) / saeg-2 (syb777)) TCGGCACGAAATATGTTG	IDT	N/A
PCR 5-RV: saeg-2 (pig5) / saeg-2 (syb776) / saeg-2 (syb777) AGATAGCATCTACCGGGTGCC	IDT	N/A
PCR 6-FWD: rde-4(ne299) CTAAGGCTGTCTATCAAAAGACGCCA	IDT	N/A
PCR 6-RV: rde-4(ne299) AAATACCAGGTGGAAATTCAGCACTTG	IDT	N/A
PCR -FWD: hrde-1 (tm1200) TCCACGTCCAATCCTTTGAG		N/A
PCR -RV: hrde-1 (tm1200) AGTGGAAAGAGTCACCACTTC	IDT	N/A
PCR 7-FWD: pigSi3[cb-unc-119(+,Psng-1::rde-4:SL2:yfp] insert TCTCACTCGTTTAGGCTATTCC	IDT	N/A
PCR 7-RV-1: pigSi3[cb-unc-119(+,Psng-1::rde-4:SL2:yfp] insert ACCCGATGAAATACGGATGC	IDT	N/A
PCR 7-RV-2: pigSi3[cb-unc-119(+,Psng-1::rde-4:SL2:yfp] insert TGAGCACAATGGGAATACATCAG	IDT	N/A
PCR 75-RV-2: pigSi3[cb-unc-119(+,Psng-1::rde-4:SL2:yfp] insertPsng-1 TGAGCACAATGGGAATACATCAG	IDT	N/A
hrde-1 sgRNA 1: 5′ GGTGTCTATGGAAACCGAGG 3′	IDT	N/A
hrde-1 sgRNA 2: 5′ CATACGATTAGCCTCCTCCT 3′,	IDT	N/A
rol-6sgRNA: 5′ GTGAGACGTCAACAATATGG 3′	IDT	N/A
rol-6(su1006) conversion template: 5′ TGTGGGTTGATATGGTTAAAC TTGGAGCAGGAACCGCTTCCAACCGT GTGCGCTGCCAACAATAT GGAGGATATGGAGCCACTGGTGTTCAGCCACCAGCACCAAC 3′.	IDT	N/A
saeg-2 sgRNA 1: CCAGCTAGCATGACTGCCACTTT saeg-2 sgRNA 2: CCACGAATGTTTAGAGTAAGTAA	SunyBiotech	N/A
saeg-2 sgRNA 3: AGACGATGCACCATCTTCGTGT TTTAG AGCTAGA AATAGCAAGT saeg-2 sgRNA 4: TGGATCTAATGAGACGGGTAGTTT TAGAGCTAGAAATAGCAAGT saeg-2 sgRNA 5: CAATGAACGAAGT CATTCGGGTTT TAGAGCTAGAAATAGCAAGT saeg-2 sgRNA 6: GAA TGTTTAGAGTAAGTAACGTTTT AGAGCTAGAAATAGCAAGT	IDT	N/A
Software and Algorithms
RMA algorithm with Partek Genomic suite v6.6	Partek	N/A
FastQC	Andrews, 2010	N/A
Cutadapt	Martin, 2011	N/A
Shortstack	Axtell, 2013	N/A
Butter	Axtell, 2014	N/A
HTSeq count	Anders et al., 2015	N/A
R Deseq2	Love et al., 2014	N/A
FISH-quant	Mueller et al., 2013	N/A
Fiji	ImageJ	N/A