| Antibodies |
| anti-GFP mAb-agarose |
MBL |
Cat# D153–8; RRID:AB_591815 |
| anti-FLAG |
Sigma |
Cat# F1804; RRID:AB_262044 |
| Bacterial Strains |
|
E. coli OP50 |
Gary Ruvkun (Harvard Medical School) |
N/A |
|
E. coli HT115 |
Gary Ruvkun (Harvard Medical School) (Kamath et al., 2003) |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| Trizol |
Life Technologies |
15596018 |
| RNA 5′ polyphosphatase |
Illumina |
RP8092H |
| NEBNext 2X PCR Master Mix |
NEB |
M0541L |
| TURBO DNase |
Life Technologies |
AM2238 |
| AMPure XP Beads |
Beckman Coulter |
A63881 |
| Pierce Protease Inhibitor Tablets |
Pierce Biotechnology |
88266 |
| Amersham Hybond -N+ Membranes |
GE Healthcare |
RPN303B |
| PerfectHyb Plus Hybridization Buffer |
Sigma-Aldrich |
H7033 |
| T4 Polynucleotide Kinase (3′ phosphatase minus) |
NEB |
M0236S |
| SureBeads Protein G Magnetic Beads |
Bio-Rad |
161–4023 |
| Critical Commercial Assays |
| TaqMan |
Life Technologies |
4366596, 4444557, 4427975 |
| NEBNext Ultra II Directional RNA Library Prep Kit for Illumina |
NEB |
E7760S |
| RNA Clean & Concentrator |
Zymo Research |
R1015 |
| Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) |
Illumina |
MRZH11124 |
| NEBNext Small RNA Library Prep Kit for Illumina |
NEB |
E7300S or E7580S |
| Deposited Data |
| NGS data |
This Study |
Gene Expression Omnibus GSE137734
|
| Experimental Models: Organisms/Strains |
|
C. elegans Bristol Strain |
CGC |
N2 |
| glp-4(bn2) I |
CGC |
SS104 |
| henn-1(pk2295) III |
René Ketting (IMB Mainz) |
NL4415 |
| prg-1(n4357) I |
CGC |
SX922 |
| rde-1(ne219) V |
CGC |
WM27 |
| mut-14(mg464) smut-1(tm1301) V |
Phillips et al., 2015 |
GR1948 |
| mut-16(pk710) I |
CGC |
NL1810 |
| henn-1(pk2452) III |
René Ketting (IMB Mainz) |
RFK30 |
| glh-1(sam24[glh-1::gfp::3Xflag]) I |
Dustin Updike (MDI) |
DUP64 |
| glh-1(sam24[glh-1::gfp::3Xflag]) I; henn-1(pk2295) III |
This Study |
TAM56 |
| rde-1(cmp133[(gfp + loxP + 3xFLAG)::rde-1]) V |
This Study |
USC1080 |
| mut-16(cmp41[mut-16::mCherry + loxP]) wago-1(cmp92[(GFP + loxP + 3xFLAG)::wago-1]) I |
This Study |
USC988 |
| henn-1(ram13[henn-1ko; mCherry::Flag-no-stop-codon]) III |
This Study |
TAM18 |
| mut-16(pk710) I; henn-1(pk2295) III |
This Study |
TAM26 |
| mut-16(pk710) I; henn-1(ram13) III |
This Study |
TAM36 |
| henn-1(pk2295) III; mut-14(mg464) smut-1(tm1301) V |
This Study |
TAM27 |
| henn-1(ram13) III; mut-14(mg464) smut-1(tm1301) V |
This Study |
TAM35 |
| flag::hrde-1([flag::hrde-1, cb-unc-119(+)]) II; unc-119(ed3) III |
Craig Mello (University of Massachusetts) (Shirayama et al., 2012) |
N/A |
| Oligonucleotides |
| See Table S5
|
See Table S5
|
N/A |
| Recombinant DNA |
| pDD282 (GFP::3xFLAG repair template plasmid) |
Addgene (Dickinson et al., 2015) |
66823 |
| pRB1017 (Guide RNA plasmid) |
Addgene (Arribere et al., 2014) |
59936 |
| pJJR83 (mCherry::3xFLAG repair template plasmid) |
Addgene (a gift from Mike Boxem) |
75028 |
| pDD162 (Guide RNA plasmid) |
Addgene (Dickinson et al., 2013) |
47549 |
| L4440 (RNAi vector) |
Addgene (a gift from Andrew Fire) |
1654 |
| pos-1 RNAi plasmid |
Gary Ruvkun (Harvard Medical School) (Kamath et al., 2003) |
N/A |
| Software and Algorithms |
| CASHX v. 2.3 |
Fahlgren et al., 2009 |
N/A |
| DESeq2 v. 1.18.1 |
Love et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Trimmomatic v. 0.35 |
Bolger et al., 2014 |
http://www.usadellab.org/cms/?page=trimmomatic |
| Star v. 2.5.0a |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR |
| Bowtie |
Langmead, 2010 |
http://bowtie-bio.sourceforge.net/index.shtml |
| RSEM v. 1.3.0 |
Li and Dewey, 2011 |
https://deweylab.github.io/RSEM/ |
| Zen Image Analysis |
Zeiss |
N/A |
