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. Author manuscript; available in PMC: 2022 Aug 26.
Published in final edited form as: Cell Rep. 2022 Aug 9;40(6):111154. doi: 10.1016/j.celrep.2022.111154

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and virus strains
E. coli OP50 CGC https://cgc.umn.edu/strain/OP50
Chemicals, peptides, and recombinant proteins
Sodium Hypochlorite Solution (5.65–6%/Laboratory) Fisher Scientific Cat#SS290-1
Sodium Hydroxide Fisher Scientific Cat#AC206060010
Cholesterol Fisher Scientific Cat#AAA1147018
Alt-R® S.p. Cas9 Nuclease V3, 100 μg IDT Cat#1081058
Nuclease Free Duplex Buffer IDT Cat#11-01-03-01
Alt-R® CRISPR-Cas9 tracrRNA, 5 nmol IDT Cat#1072532
Edit-R CRISPR-Cas9 Synthetic tracrRNA Horizon Discovery Cat#U-002005-20
RNAse H NEB Cat#M0297L
TRIzol™ LS Reagent ThermoFisher CAT#10296010
TRIzol Reagent ThermoFisher Cat#15596018
TaqMan™ Universal Master Mix II, with UNG ThermoFisher Cat#4440038
Critical commercial assays
TaqMan™ MicroRNA Reverse Transcription Kit ThermoFisher Cat#4366596
NEBNext®Multiplex Small RNA Library Prep Kit for Illumina® NEB Cat#E7560S
TaqMan™ MicroRNA Assay ThermoFisher Cat#4440886
Deposited data
Raw sequence data This study Deposited in NCBI Sequence Read Archive (SRA) under accession number SRA:PRJNA782102.
Experimental models: Organisms/strains
See Table S2 for oligonucleotides. N/A N/A
C. elegans:mir-35(seed_rev): mir-35(cdb2 cdb4) II Yang et al. (2020b) Genes and Development MCJ11
C. elegans:mir-35(seed_mut): mir-35(cdb2 cdb6) II This paper MCJ13
C. elegans:mir-35(mut_3′): mir-35(cdb2 cdb72) II This paper MCJ180
C. elegans:mir-35(mir-82_3′): mir-35(cdb2 cdb78) II This paper MCJ191
C. elegans: mir-35(seed_rev_no_bulge): mir-35(cdb2 cdb95) II This paper MCJ211
C. elegans: mir-35(seed_rev); egl-1, nhl-2, sup-26(seed_rev): mir-35(cdb2 cdb4) II; sup-26(cdb99) nhl-2(cdb100) III; egl-1(cdb97) V This paper MCJ218
C. elegans: mir-35(wild_type); egl-1, nhl-2, sup-26(seed_rev): sup-26(cdb99) nhl-2(cdb100) III; egl-1(cdb97) V This paper MCJ219
C. elegans: ebax-1(null): ebax-1(tm2321) IV Wang et al. (2013) Neuron CZ9907
See Table S2 for allele information. N/A N/A
Oligonucleotides
See Table S2 for oligonucleotides. N/A N/A
Software and algorithms
SnapGene 5 SnapGene www.snapgene.com
Adobe Illustrator 26 Adobe Inc. https://www.adobe.com/products/illustrator.html
Prism 9 GraphPad https://www.graphpad.com/scientific-software/prism/
Cutadapt 3.4 Martin (2011) https://cutadapt.readthedocs.io/en/stable/
bowtie2 2.4.4 Langmead et al. (2009) http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
samtools 1.13 Danecek et al. (2021) https://sourceforge.net/projects/samtools/files/samtools/
htseq 0.13.5 Anders et al. (2015) https://pypi.python.org/pypi/HTSeq
Tailor Package Chou et al. (2015) https://github.com/jhhung/Tailor
TargetScan 7.0 Agarwal et al. (2015) https://www.targetscan.org/vert_70/
DESeq2 Love et al. (2014) https://bioconductor.org/packages/release/bioc/html/DESeq2.html