| Strain, strain background (Escherichia coli) |
OP50 |
CaenorhabditisGenetics Center |
|
|
| Strain, strain background (Escherichia coli) |
HT115 |
CaenorhabditisGenetics Center |
|
|
| Strain, strain background (Escherichia coli) |
BL21 (DE3) |
ThermoFisher Scientific |
EC0114 |
Chemically competent |
| Strain, strain background (Escherichia coli)
|
XL1-Blue |
Agilent |
200,249 |
Chemically competent |
| Strain, strain background (Pseudomonas aeruginosa) |
UCBPP-PA14 |
PMID:7604262
|
|
|
| Strain, strain background (Caenorhabditis elegans) |
N2; wild-type |
CGC, PMID:4366476
|
WormBase ID:WBStrain00000001 |
Laboratory reference strain/wild type |
| Strain, strain background (Caenorhabditis elegans) |
KU25 |
PMID:15116070/ |
WormBase ID: WBStrain00024040 |
Genotype: pmk-1(km25) IV
|
| Strain, strain background (Caenorhabditis elegans) |
AU3 |
PMID:12142542
|
WormBase ID: WBStrain00000259 |
Genotype: nsy-1(ag3) II
|
| Strain, strain background (Caenorhabditis elegans) |
ZD101 |
PMID:19837372
|
WormBase ID:WBStrain00040806 |
Genotype: tir-1(qd4) III
|
| Strain, strain background (Caenorhabditis elegans) |
AA968 |
PMID:23931753
|
|
Genotype: nhr-8(hd117) IV
|
| Strain, strain background (Caenorhabditis elegans) |
AE501 |
PMID:11516648
|
WormBase ID:WBStrain00000059 |
Genotype: nhr-8(ok186) IV
|
| Strain, strain background (Caenorhadbditis elegans) |
AU78 |
PMID:19837372
|
WormBase ID:WBStrain00000262 |
Genotype: agIs219 [T24B8.5p::gfp::unc-54–3’UTR; ttx-3p::gfp::unc-54–3’UTR] III
|
| Strain, strain background (Caenorhabditis elegans) |
AU307 |
PMID:24875643
|
|
Genotype: agIs44 [irg-4p::gfp::unc-54–3’UTR; myo-2p::mCherry] |
| Strain, strain background (Caenorhabditis elegans) |
AY101 |
PMID:20133945
|
WormBase ID:WBStrain00000322 |
Genotype: acIs101 [pDB09.1(irg-5p::gfp); pRF4(rol-6(su1006))] |
| Strain, strain background (Caenorhabditis elegans) |
TJ356 |
PMID:11747825
|
WormBase ID:WBStrain00034892 |
Genotype: zIs356 [daf-16p::daf-16a/b::gfp + pRF4(rol-6(su1006))] |
| Strain, strain background (Caenorhabditis elegans) |
RPW278 |
This study |
|
Genotype: nhr-8(hd117);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW317 |
This study |
|
Genotype: tir-1(qd4);nhr-8(hd117)
|
| Strain, strain background (Caenorhabditis elegans) |
RPW339 |
This study |
|
Genotype: tir-1(ums47[E788A]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW369 |
This study |
|
Genotype: tir-1(ums54[ΔSAM]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW374 |
This study |
|
Genotype: tir-1(ums55[G747P]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW381 |
This study |
|
Genotype: tir-1(ums56[H833A]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW386 |
This study |
|
Genotype: tir-1(ums57[tir-1::3xFLAG]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW387 |
This study |
|
Genotype: tir-1(ums58[tir-1[E788A]::3xFLAG]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW388 |
This study |
|
Genotype: tir-1 (ums59[tir-1[ΔSAM]::3xFLAG]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW 389 |
This study |
|
Genotype: tir-1(ums60[tir-1[G747P]::3xFLAG]);agIs219
|
| Strain, strain background (Caenorhabditis elegans) |
RPW403 |
This study |
|
Genotype: tir-1(ums63[tir-1::wrmScarlet])
|
| Strain, strain background (Caenorhabditis elegans) |
RPW404 |
This study |
|
Genotype: nhr-8(hd117);tir-1(ums63[tir-1::wrmScarlet])
|
| Antibody |
anti-total PMK-1(rabbit polyclonal) |
PMID:30668573
|
|
WB(1:1000) |
| Antibody |
anti-Phospho-p38 MAPK (Thr180/Tyr182)(rabbit polyclonal) |
Cell Signaling Technology |
9211 |
WB(1:1,000) |
| Antibody |
anti-FLAG(mouse monoclonal) |
Sigma-Aldrich |
F1804 |
WB(1:1,000) |
| Antibody |
anti-alpha-tubulin (mouse monoclonal) |
Sigma-Aldrich |
T5168 |
WB(1:2,000) |
| Antibody |
anti-mouse IgG-HRP (goat polyclonal) |
Abcam |
ab6789 |
WB(1:10,000) |
| Antibody |
anti-rabbit IgG-HRP(goat polyclonal) |
Cell Signaling Technology |
7074 |
WB(1:10,000) |
| Chemical compound, drug |
Peptone |
Gibco |
211820 |
|
| Chemical compound, drug |
Agar |
Fisher |
BP9744 |
|
| Chemical compound, drug |
Cholesterol |
Sigma Aldrich |
C3045 |
|
| Chemical compound, drug |
Tri-Reagent |
Sigma Aldrich |
T9424 |
|
| Chemical compound, drug |
TERGITOL solution (Type NP-40) |
Sigma Aldrich |
NP40S |
|
| Chemical compound, drug |
RIPA Buffer |
Cell Signaling Technology, Inc |
89900 |
|
| Chemical compound, drug |
Halt Protease and Phosphatase inhibitor |
ThermoFisher Scientific |
78445 |
|
| Chemical compound, drug |
NuPAGELDS sample buffer |
ThermoFisher Scientific |
NP0007
|
|
| Chemical compound, drug |
1,6-hexanediol |
Sigma Aldrich |
240117 |
|
| Chemical compound, drug |
Nicotinamide 1,N6-ethenoadenine dinucleotide; ε-NAD |
Sigma Aldrich |
N2630 |
|
| Chemical compound, drug |
PEG 400 |
Sigma Aldrich |
91893 |
|
| Chemical compound, drug |
PEG 1500 |
Sigma Aldrich |
86101 |
|
| Chemical compound, drug |
PEG 3350 |
Sigma Aldrich |
88276 |
|
| Chemical compound, drug |
PEG 8000 |
Sigma Aldrich |
89510 |
|
| Chemical compound, drug |
Dextran |
Fisher Scientific |
ICN16011010 |
|
| Chemical compound, drug |
Sucrose |
Sigma Aldrich |
S0389 |
|
| Chemical compound, drug |
Glycerol |
Sigma Aldrich |
G5516 |
|
| Chemical compound, drug |
Sodium citrate |
Sigma Aldrich |
S4641 |
|
| Chemical compound, drug |
Kanamycin |
Research Products International |
K22000 |
|
| Chemical compound, drug |
IPTG |
ThermoFisher Scientific |
R0392 |
|
| Chemical compound, drug |
Pierce EDTA-free protease inhibitor mini tablets |
ThermoFisher Scientific |
A32955 |
|
| Commercial assay or kit |
iProof High-Fidelity DNA Polymerase |
Bio-Rad Laboratories, Inc |
172–5301 |
|
| Commercial assay or kit |
iScript gDNA Clear cDNA Synthesis Kit |
Bio-Rad Laboratories, Inc |
172–5034 |
|
| Commercial assay or kit |
iTaq Universal SYBR Green Supermix |
Bio-Rad Laboratories, Inc |
1725120 |
|
| Commercial assay or kit |
DreamTaq Green PCR |
ThermoFisher Scientific |
K1081 |
|
| Commercial assay or kit |
DC protein assay |
Bio-Rad Laboratories, Inc |
5000116 |
|
| Commercial assay or kit |
NuPAGE 4%–12% BisTris gels |
ThermoFisher Scientific |
NP0321BOX |
|
| Commercial assay or kit |
NuPAGE 3%–8% TrisAcetate gels |
ThermoFisher Scientific |
EA0375BOX |
|
| Commercial assay or kit |
SuperSignal West Pico PLUS Chemiluminescent Substrate |
Thermo Fisher Scientific |
34577 |
|
| Commercial assay or kit |
SuperSignal West Femto PLUS Chemiluminescent Substrate |
Thermo Fisher Scientific |
34095 |
|
| Commercial assay or kit |
Strep-Tactin XT Superflow high-capacity resin |
IBA Lifesciences |
2-4030-025 |
Product discontinued; suitable replacement is Strep-Tactin XT 4Flow high capacity resin (2-5030-025) |
| Commercial assay or kit |
Wizard Plus SV Minipreps DNA Purification System |
Promega |
A1460 |
|
| Commercial assay or kit |
TALON Metal Affinity Resin |
Takara |
635,502 |
|
| Peptide, recombinant protein |
Lysozyme |
Sigma Aldrich |
L6876 |
|
| Peptide, recombinant protein |
DpnI |
NEB |
R0176S |
|
| Peptide, recombinant protein |
ADP-ribosyl cyclase |
Sigma Aldrich |
A9106 |
|
| Peptide, recombinant protein |
SpCas9 Nuclease |
IDT |
1081058 |
|
| Recombinant DNA reagent |
pET-30a(+) TIR (plasmid) |
Loring et al., 2021
|
|
Referred to as pET30a+ Strep-ceTIR-HIS in reference |
| Software, algorithm |
Fiji/imageJ |
PMID:22743772
|
|
|
| Software, algorithm |
OASIS 2 |
PMID:27528229
|
|
|
| Software, algorithm |
R Console (Version 3.5) |
The R Foundation |
|
https://www.r-project.org/
|
| Software, algorithm |
FastQC (Version 0.11.5) |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
|
|
| Software, algorithm |
Kallisto (version 0.45.0) |
PMID:27043002
|
|
|
| Software, algorithm |
Sleuth (version 0.30.0) |
PMID:28581496
|
|
|
| Software, algorithm |
GSEA (version 4.1.0) |
PMID:16199517
|
|
|
| Software, algorithm |
pheatmap (version 1.0.12) |
https://cran.r-project.org/web/packages/pheatmap/index.html
|
|
|
| Software, algorithm |
DAVID Bioinformatics database |
PMID:19131956
|
|
|
| Software, algorithm |
GraphPad Prism 9 |
Graphpad |
|
https://www.graphpad.com/scientific-software/prism/
|
