Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Chemical compound, drug | Levamisole hydrochloride | Sigma | L0380000 | |
| Chemical compound, drug | Trizol Reagent | Life Technologies | 15596026 | |
| Chemical compound, drug | Phenol Chloroform Isoamyl | Sigma | P2069 | |
| Other | Heavy Phase Lock tube | QuantaBio | 23028330 | |
| Chemical compound, drug | Ultra Pure Glycogen | ThermoFisher | 10814010 | |
| Peptide, recombinant protein | RNA 5' Polyphosphatase | Epicenter | RP8092H | |
| Commercial assay, kit | NEBNext Multiplex Small RNA Library Prep Set for Illumina | New England Biolabs | E7300 | |
| Commercial assay, kit |
TapeStation screen tapes |
Agilent |
5067–5582 | |
| 5067–5588 | ||||
| Commercial assay, kit |
TapeStation reagents |
Agilent |
5067–5583 | |
| 5067–5589 | ||||
| Chemical compound, drug | E-Gel 4% agarose | Life Technologies | G401004 | |
| Commercial assay, kit | MinElute DNA purification kit | Qiagen | 28006 | |
| Chemical compound, drug | RNase free Nuclease-free water | Ambion | AM9932 | |
| Peptide, recombinant protein | NlaIII | New Englang BioLabs (NEB) | 631207 | |
| Commercial assay, kit | TG NextSeq 500/550 High Output Kit v2 (75 cycles) | Illumina | TG-160–2005 | |
| Strain, strain background (Caenorhabditis elegans) | C. elegans: Strain SX1263: unc-119(ed3) III; mex-5::gfp::h2b::tbb-2 II | The Eric Miska lab (Sapetschnig et al., 2015) | SX1263 | |
| Strain, strain background (C. elegans) | C. elegans: Strain EG6089: unc-119(ed3) III; oxTi38[cb-unc-119(+) Ppie-1::GFP] IV | The Eric Miska lab (Sapetschnig et al., 2015) | EG6089 | |
| Strain, strain background (C. elegans) | C. elegans: Strain JA1527: weSi14 [Pmex-5::mCherry::(Gly)5Ala/his-58/tbb-2 3′UTR; cb-unc-119(+)] IV | The Julie Ahringer lab (Zeiser et al., 2011) | JA1527 | |
| Strain, strain background (C. elegans) | C. elegans: Strain GR1720: mgSi4 [(pCMP2) ubl-1p::GFP::siR-1-sensor-ubl-1–3'UTR + Cbr-unc-119(+)] IV | Caenorhabditis Genetics Center | WB strain: GR1720 | |
| Strain, strain background (C. elegans) | C. elegans: Strain KB3: kgb-1 (um3) IV | Caenorhabditis Genetics Center | KB3 | |
| Strain, strain background (C. elegans) | C. elegans: Strain KB3: kgb-1 (um3) IV crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain FK171: mek-1(ks54); sek-1(qd127) | Caenorhabditis Genetics Center | FK171 | |
| Strain, strain background (C. elegans) | C. elegans: Strain FK171: mek-1(ks54); sek-1(qd127) X crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain CF1038: daf-16(mu86) I | Caenorhabditis Genetics Center | CF1038 | |
| Strain, strain background (C. elegans) | C. elegans: Strain CF1038: daf-16(mu86) I, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain KU4: sek-1(km4) X | Caenorhabditis Genetics Center | KU4 | |
| Strain, strain background (C. elegans) | C. elegans: Strain KU4: sek-1(km4) X, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain KU25: pmk-1(km25) IV | Caenorhabditis Genetics Center | KU25 | |
| Strain, strain background (C. elegans) | C. elegans: Strain KU25: pmk-1(km25) IV, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain MR1175: aak-1(tm1944) III, aak-2(ok524) X | The Richard Roy lab (Demoinet et al., 2017) | MR1175 | |
| Strain, strain background (C. elegans) | C. elegans: Strain MR1175: aak-1(tm1944) III, aak-2(ok524) X, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain PS355: hsf-1(sy441) I | Caenorhabditis Genetics Center | PS355 | |
| Strain, strain background (C. elegans) | C. elegans: Strain PS355: hsf-1(sy441) I, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain CB1370: daf-2(e1370) III | Caenorhabditis Genetics Center | CB1370 | |
| Strain, strain background (C. elegans) | C. elegans: Strain CB1370: daf-2(e1370) III, crossed with Strain EG6089 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain QV225: skn-1(zj15) IV | Caenorhabditis Genetics Center | QV225 | |
| Strain, strain background (C. elegans) | C. elegans: Strain QV225: skn-1(zj15) IV, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain MT13293: met-2(n4256) III | Caenorhabditis Genetics Center | MT13293 | |
| Strain, strain background (C. elegans) | C. elegans: Strain MT13293: met-2(n4256) III, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain RB1789: met-2(ok2307) III | Caenorhabditis Genetics Center | RB1789 | |
| Strain, strain background (C. elegans) | C. elegans: Strain RB1789: met-2(ok2307) III, crossed with Strain SX1263 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain KU4: sek-1(km4) X, crossed with strain JA1527 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain ZD202: sek-1(km4) X; qdEx8[unc-119p::sek-1(cDNA)::GFP::unc-54–3' UTR + myo-2p::mStrawberry::unc-54–3' UTR], crossed with strain JA1527 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain ZD193: sek-1(km4) X; qdEx4 [ges-1p::sek-1(cDNA)::GFP::unc-54–3' UTR + myo-2p::mStrawberry::unc-54–3' UTR], crossed with strain JA1527 | This study | ||
| Strain, strain background (C. elegans) | C. elegans: Strain OH14221: met-2(ot861[met-2::mKate2]) III | Caenorhabditis Genetics Center (Patel and Hobert, 2017) | OH14221 | |
| Strain, strain background (C. elegans) | C. elegans: Strain OH14221: met-2(ot861[met-2::mKate2]) III crossed with strain QV225 | This study | ||
| Sequence-based reagent | PCR 1-FWD: mek-1/sek-1 | IDT | TTTCCATCAACTCAGTCGCCG | |
| Sequence-based reagent | PCR 1-REV1: mek-1/sek-1 | IDT | TTCATTAGTCAATTGGGTCAG | |
| Sequence-based reagent | PCR 1-REV2: mek-1/sek-1 | IDT | CACTTTTCAATTAAGGTACAAC | |
| Sequence-based reagent | PCR 2-FWD: kgb-1 | IDT | CCCTACTTTATAATGAGATGC | |
| Sequence-based reagent | PCR 2-REV1: kgb-1 | IDT | TTCATTAGTCAATTGGGTCAG | |
| Sequence-based reagent | PCR 2-REV2: kgb-1 | IDT | CACTTTTCAATTAAGGTACAAC | |
| Sequence-based reagent | PCR 3-FWD: daf-16 | IDT | GTTCAGTAGACGGTGACCATCT | |
| Sequence-based reagent | PCR 3-REV1: daf-16 | IDT | GCTTCGGCTTGAAAGATCAGTG | |
| Sequence-based reagent | PCR 3-REV2: daf-16 | IDT | GTACGCCGTGGTCCGACTA | |
| Sequence-based reagent | PCR 4-FWD: skn-1 | IDT | GAAGAGAATGCTCGATATGAAG | |
| Sequence-based reagent | PCR 4-REV: skn-1 | IDT | TTTCAGTCGTTTATAAGAGAGC | |
| Sequence-based reagent | PCR 5-FWD: aak-1 | IDT | ATCGATACGGAACCAACTG | |
| Sequence-based reagent | PCR 5-REV: aak-1 | IDT | GGGTATGGTAGTACCAATAGG | |
| Sequence-based reagent | PCR 6-FWD: aak-2 | IDT | CGATAGCACAGACAACAGTTCG | |
| Sequence-based reagent | PCR 6-REV: aak-2 | IDT | GATGGTGGCCCTCTTCATC | |
| Sequence-based reagent | PCR 7-FWD1: daf-18 | IDT | AGGGTAATGCATTTCAGCAC | |
| Sequence-based reagent | PCR 7-FWD2: daf-18 | IDT | CCCGCATATAAACTGGAAATGTG | |
| Sequence-based reagent | PCR 7-REV: daf-18 | IDT | CAAATACGTCAGTTTCAACGTG | |
| Sequence-based reagent | PCR 8-FWD: pmk-1 | IDT | CTATAAGTTGCCATGACCTC | |
| Sequence-based reagent | PCR 8-REV: pmk-1 | IDT | GCTCCCATCAACATTGATAC | |
| Sequence-based reagent | PCR 9-FWD1: sek-1 | IDT | CTAGAATAAGTGCTATGCTAG | |
| Sequence-based reagent | PCR 9-FWD2: sek-1 | IDT | GTTGTCTAAGTATAATTGTCC | |
| Sequence-based reagent | PCR 9-REV: sek-1 | IDT | TGATTGATTATAACTACGAGG | |
| Sequence-based reagent | PCR 10-FWD1: met-2 | IDT | TTTACTGTCACATCACCTGC | |
| Sequence-based reagent | PCR 10-FWD2: met-2 | IDT | AAGCAGATGTTTGTCAGAATCC | |
| Sequence-based reagent | PCR 10-REV: met-2 | IDT | AGCAGCATTCATCTTCGC | |
| Software, algorithm | FastQC | Andrews, 2010 | ||
| Software, algorithm | Cutadapt | Martin, 2011 | ||
| Software, algorithm | Shortstack | Shahid and Axtell, 2014 | ||
| Software, algorithm | HTSeq count | Anders et al., 2014 | ||
| Software, algorithm | R Deseq2 | Love et al., 2014 | ||
| Software, algorithm | RNAlysis | Teichman, 2019 | Version 1.3.5 | |
| Software, algorithm | Fiji | Schindelin et al., 2012 | ||
| Software, algorithm | MATLAB R2018b | MATLAB | Version R2018b | |
| Software, algorithm | IoSR-Surry MatlabToolbox (BoxPlot function) | Institute of Sound Recording, University of Surrey | https://github.com/IoSR-Surrey/MatlabToolbox | Version 2.8 |
| Software, algorithm | GraphPad Prism 8 | GraphPad Software | http://www.graphpad.com/ | Version 8.0.0 |