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. Author manuscript; available in PMC: 2020 May 12.
Published in final edited form as: Cell Rep. 2020 Apr 7;31(1):107478. doi: 10.1016/j.celrep.2020.03.042

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Total PMK-1 Antibody Peterson et al., 2019 N/A
Anti-p38 MAPK, phospho (Thr180 / Tyr182) Antibody, Unconjugated Cell Signaling Technology Cat# 9211
RRID:AB_331641
Lot# 25
Monoclonal Anti-alpha-Tubulin antibody produced in mouse Sigma-Aldrich Cat# T5168
RRID:AB_477579
Lot# 038M4813V
Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology Cat# 7074
RRID:AB_2099233
Lot# 28
Goat Anti-Mouse IgG - H&L Polyclonal Antibody, HRP Conjugated Abcam Cat# ab6789
RRID:AB_955439
Lot# GR3216437–2
Bacterial and Virus Strains
Escherichia coli OP50 Brenner, 1974 RRID:WB-STRAIN:OP50
Pseudomonas aeruginosa (UCBPP-PA14) Rahme et al., 1995 RRID:WB-STRAIN:PA14
Chemicals, Peptides, and Recombinant Proteins
5-Fluoro-2-deoxyuridine Sigma-Aldrich Cat# CAF0503
(—) Tetramisole hydrochloride Sigma-Aldrich Cat# L9756–10G
EcoRI Restriction Enzyme New England BioLabs Cat# R0101
Q5 High-Fidelity DNA Polymerase New England BioLabs Cat# M0491S
Isopropyl-β-D-thiogalactoside Research Products International CAT# L56000
Trizol Thermo Fisher Scientific Cat# 15596018
Proteinase K New England BioLabs Cat# P8107S
Phenol:chloroform:isoamyl alcohol Thermo Fisher Cat# 15593031
Critical Commercial Assays
Gibson Assembly Cloning Kit New England BioLabs Cat# E5510S
iScript gDNA Clear cDNA Synthesis Kit Bio-Rad Cat# 172–5034
iTaq Universal SYBR Green Supermix Bio-Rad Cat# 1725120
Deposited Data
Raw and analyzed mRNA-Seq data This study GEO:GSE130959
Experimental Models: Organisms/Strains
C. elegans: Strain: N2 (Bristol) Caenorhabditis Genetics Center WB Cat# WBStrain00000001;
RRID:WB-STRAIN:WBStrain00000001
C. elegans: Strain: KU25 pmk-1(km25) Kim et al., 2002 WB Cat# WBStrain00024040;
RRID:WB-STRAIN:WBStrain00024040
C. elegans: Strain: AU306 agIs44
[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry] 		Pukkila-Worley et al., 2014 N/A
C. elegans: Strain: AY101 acIs101
[PDB09.1(Pirg-5::GFP); pRF4(rol-6(su1006))] 		Bolz et al., 2010 WB Cat# WBStrain00000322;
RRID:WB-STRAIN:WBStrain00000322
C. elegans: Strain: RPW40 olrn-1(ums9); agIs44
[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry] 		This study N/A
C. elegans: Strain: RPW31 olrn-1(ums11); agIs44
[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry] 		This study N/A
C. elegans: Strain: RPW222 olrn-1(ky626); agIs44
[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry] 		This study N/A
C. elegans: Strain: RPW211 olrn-1(ums9); acIs101
[PDB09.1(Pirg-5::GFP); pRF4(rol-6(su1006))] 		This study N/A
C. elegans: Strain: ZD101 tir-1(qd4) Shivers et al., 2009 WB Cat# WBStrain00040806; RRID:WB-STRAIN:WBStrain00040806
C. elegans: Strain: RPW43 nsy-1(ums8);
agIs44[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry] 		Cheesman et al., 2016 WormBase ID: WBVar02145386
C. elegans: Strain: RPW 129 olrn-1(ums9);pmk-1(km25) This study N/A
C. elegans: Strain: RPW189 olrn-1(ums9);tir-1(qd4);
agIs44[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry] 		This study N/A
C. elegans: Strain: RPW131 orln-1(ums9);
agIs44[Pirg-4::GFP::unc-54–3′UTR; Pmyo-2::mCherry];
umsEx4 [Porln-1::orln-1;3′UTRorln-1; Pmyo-3::mCherry] 		This study N/A
C. elegans: Strain: RPW133 orln-1(ums9);
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry];umsEx6 [Porln-1::orln-1;3′UTRorln-1;
Pmyo-3::mCherry] 		This study N/A
C. elegans: Strain: RPW134 orln-1(ums9);
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry];umsEx7 [Porln-1::orln-1;3′UTRorln-1;
Pmyo-3::mCherry] 		This study N/A
C. elegans: Strain: RPW159 orln-1(ums9);
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry];umsEx20 [Psng-1::orln-1;3′UTRorln-1;
Pmyo-3::mCherry] 		This study N/A
C. elegans: Strain: RPW160 orln-1(ums9);
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry];umsEx21 [Psng-1::orln-1;3′UTRorln-1;
Pmyo-3::mCherry] 		This study N/A
C. elegans: Strain: RPW162 orln-1(ums9);
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry];umsEx23 [Psng-1::orln-1;3′UTRorln-1;
Pmyo-3::mCherry] 		This study N/A
C. elegans: Strain: CX7517 olrn-1(ky626); kyEx914
[Podr-3::olrn-1;Podr-1::mCherry;coel::GFP] 		Bauer Huang et al., 2007 Laboratory of Cornelia
Bargmann: Strain ID CX7517
C. elegans: Strain: CX7521 olrn-1(ky626); kyEx918
[Podr-3::olrn-1;Podr-1::mCherry;coel::GFP] 		Bauer Huang et al., 2007 Laboratory of Cornelia
Bargmann: Strain ID CX7521
C. elegans: Strain: olrn-1(ky626) Bauer Huang et al., 2007 WormBase ID: WBVar00088455
C. elegans: Strain: RPW207
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry]; umsEx4
(Porln-1::orln-1;3′UTRorln-1; Pmyo-3::mCherry) 		This study N/A
C. elegans: Strain: RPW209
agIs44[Pirg-4::GFP::unc-54–3′UTR;
Pmyo-2::mCherry]; umsEx21
(Psng-1::orln-1;3′UTRorln-1; Pmyo-3::mCherry) 		This study N/A
C. elegans: Strain: RPW216 atf-7(qd22 qd130);
agIs219[T24B8.5::GFP]; olrn-1(ums9) 		This study N/A
C. elegans: Strain: RPW218 orln-1
(ums9); pmk-1(km25); acEx102
[vha-6p::pmk-1::GFP + rol-6(su1006)] 		This study N/A
C. elegans: Strain: AY102 pmk-1(km25); acEx102
[vha-6p::pmk-1::GFP + rol-6(su1006)] 		Bolz et al., 2010 WB Cat# WBStrain00000323;
RRID:WB-STRAIN:WBStrain000003233
C. elegans: Strain: ZD193 sek-1(km4);qdEx4
[Pges-1::sek-1(cDNA)::GFP::unc-54-3′
UTR + myo-2p::mStrawberry::unc-54-3′ UTR] 		Shivers et al., 2009 WB Cat# WBStrain00040807;
RRID:WB-STRAIN:WBStrain00040807
C. elegans: Strain: ZD202 sek-1(km4);qdEx8
[Punc-119::sek-1(cDNA)::GFP::unc-54-3′
UTR + myo-2p::mStrawberry::unc-54-3′ UTR] 		Shivers et al., 2009 WB Cat# WBStrain00040808;
RRID:WB-STRAIN:WBStrain00040808
C. elegans: Strain: RPW220 olrn-1(ums9); sek-1(km4); agIs44 This study N/A
C. elegans: Strain: RPW227 olrn-1(ums9); sek-1(km4); agIs44; qdEx4 This study N/A
C. elegans: Strain: RPW224 olrn-1(ums9); sek-1(km4); agIs44; qdEx8 This study N/A
C. elegans: Strain: CX5757 kyIs140 I; nsy-4(ky616) IV. Caenorhabditis
Genetics Center		 WB Cat# WBStrain00005274;
RRID:WB-STRAIN:WBStrain00005274
C. elegans: Strain: (CX6161) inx-19(ky634) I. Caenorhabditis
Genetics Center		 WB Cat# WBStrain00005278;
RRID:WB-STRAIN:WBStrain00005278
Oligonucleotides
olrn-1 Rescue PCR FWD primer: CAGAACCAGATTCTCGGAATGA IDT N/A
olrn-1 Rescue PCR REV primer: AGAGGAAGAGAGACAGGATGAA IDT N/A
Gibson Assembly Primer for Psng-1::olrn-1b construct:
CCCCCCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGttgagcagcgactaacaaaa		 IDT N/A
Gibson Assembly Primer for Psng-1::olrn-1b construct:
ACCTGACACTAATTTCTCTTGGCGCTGAACATCTAGTCATgctaaaataaaagaaatata		 IDT N/A
Gibson Assembly Primer for Psng-1::olrn-1b construct:
atgactagatgttcagcgcc		 IDT N/A
Gibson Assembly Primer for Psng-1::olrn-1b construct:
GGCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGtttcatatatcttatgccgt		 IDT N/A
Recombinant DNA
Plasmid: pBluescript SK(−) Addgene N/A
Software and Algorithms
GraphPad Prism 8 Graphpad https://www.graphpad.com/scientific-software/prism/
OASIS 2 Han et al., 2016 https://sbi.postech.ac.kr/oasis2/
Adobe Creative Cloud Adobe https://www.adobe.com/creativecloud.html
ApE: A plasmid Editor M. Wayne Davis http://jorgensen.biology.utah.edu/wayned/ape/
Microsoft Excel Microsoft https://office.live.com/start/Excel.aspx
FastQC (Version 0.11.8) Wingett and Andrews, 2018 https://www.bioinformatics.babraham.ac.uk/projects/download.html
Multiqc (Version 1.7) Ewels et al., 2016 https://github.com/ewels/MultiQC
Trimmomatic (Version 0.36) Bolger et al., 2014 http://www.usadellab.org/cms/?page=trimmomatic
HISAT2 (Version 2.1.0) Kim et al., 2015; Pertea et al., 2016 https://ccb.jhu.edu/software/hisat2/index.shtml
Samtools (Version 1.3.1) Li, 2011; Li et al., 2009 https://sourceforge.net/projects/samtools/files/samtools/1.3.1/
Stringtie (Version 1.3.4) Pertea et al., 2015, 2016 https://ccb.jhu.edu/software/stringtie/
Ballgown (Version 3.8) Pertea et al., 2016 https://www.bioconductor.org/packages/release/bioc/html/ballgown.html
R Console (Version 3.5) The R Foundation https://www.r-project.org/