Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (C. elegans) | cdk-8 | WormBase | WBGene00000409 | |
| Gene (C. elegans) | gcn-1 | WormBase | WBGene00021697 | |
| Gene (C. elegans) | R09F10.3 | WormBase | WBGene00019987 | |
| Gene (C. elegans) | Y75B8A.8 | WormBase | WBGene00013545 | |
| Gene (C. elegans) | sfrp-1 | WormBase | WBGene00022242 | |
| Gene (C. briggsae) | Cbr-sfrp-1 | WormBase | WBGene00027904 | |
| Strain, strain background (C. briggsae) | HK104 | DOI:10.1073/pnas.0406056102 | HK104CB
WormBase ID: WBStrain00041077 |
Wild isolate. Ancestor strain of MA lines. |
| Strain, strain background (C. briggsae) | MAL211 | DOI:10.1371/journal.pgen.1000877 | MAL211 | Mutation Accumulation line (250 generations) |
| Strain, strain background (C. briggsae) | MAL296 | DOI:10.1371/journal.pgen.1000877 | MAL296 | Mutation Accumulation line (250 generations) |
| Strain, strain background (C. elegans) | N2 | DOI:10.1073/pnas.0406056102 | N2CB
WormBase ID: WBStrain00000001 |
Lab reference strain. Ancestor strain of MA lines. |
| Strain, strain background (C. elegans) | MAL516 | DOI:10.1371/journal.pgen.1000877 | MAL516 | Mutation Accumulation line (250 generations) |
| Strain, strain background (C. elegans) | PB306 | DOI:10.1073/pnas.0406056102 | PB306CB
WormBase ID: WBStrain00030546 |
Lab reference strain. Ancestor strain of MA lines. |
| Strain, strain background (C. elegans) | MAL418 | DOI:10.1371/journal.pgen.1000877 | MAL418 | Mutation Accumulation line (250 generations) |
| Strain, strain background (C. elegans) | MAL450 | DOI:10.1371/journal.pgen.1000877 | MAL450 | Mutation Accumulation line (250 generations) |
| Strain, strain background (C. elegans) | MAL488 | DOI:10.1371/journal.pgen.1000877 | MAL488 | Mutation Accumulation line (250 generations) |
| Genetic reagent (C. briggsae) |
Cbr-sfrp-1
(mf177) |
this paper | JU3707 | N59H edited allele. Background strain: HK104CB cf Suppl. File 5. |
| Genetic reagent (C. briggsae) |
Cbr-sfrp-1
(mf178) |
this paper | JU3708 | Control edited allele with synonymous mutations. Background strain: HK104CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | gcn-1(mf165) | this paper | JU3641 | Precise deletion of exon 21 as in MAL516. Background strain: N2CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | gcn-1(mf166) | this paper | JU3642 | Precise deletion of exon 21 as in MAL516. Background strain: N2CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | cdk-8(mf167) | this paper | JU3643 | V40A edited allele. Background strain: PB306CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | cdk-8(mf168) | this paper | JU3644 | V40A edited allele. Background strain: PB306CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | cdk-8(mf169) | this paper | JU3645 | Control edited allele with synonymous mutations. Background strain: PB306CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | cdk-8(mf170) | this paper | JU3646 | Control edited allele with synonymous mutations. Background strain: PB306CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | R09F10.3(mf171) | this paper | JU3647 | 16 bp deletion as in MAL488. Background strain: PB306CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | R09F10.3(mf172) | this paper | JU3648 | 16 bp deletion as in MAL488. Background strain: PB306CB cf Suppl. File 5. |
| Genetic reagent (C. elegans) | Y75B8A.8(mf139) | this paper | JU3357 | Deletion in exon 3. Background strain: PB306CB cf Suppl. File 5. |
| Recombinant DNA reagent | pJA58 (plasmid) | Addgene | Addgene:Plasmid #59933 | |
| Sequence-based reagent | Alt-R CRISPR-Cas9 tracrRNA | IDT | Cat#: 1072533 | |
| Sequence-based reagent | crRNA (for cdk-8; gcn-1; R09F10.3; sfrp-1; Y75B8A.8) | this paper | CRISPR RNA guides. Sequences provided in Suppl. File 10 | |
| Sequence-based reagent | ssDORT (for cdk-8; gcn-1; R09F10.3; sfrp-1) | this paper | Single-stranded DNA oligonucleotide repair templates.Sequences provided in Suppl. File 10 | |
| Peptide, recombinant protein | Streptococcus pyogenes Cas9 nuclease V3 | IDT | Cat#:1081058 | |
| Software, algorithm | GATK | DOI: 10.1002/0471250953.bi1110s43 | RRID:SCR_001876 | v3.6 or v3.7 |
| Software, algorithm | breakdancer | DOI:10.1038/nmeth.1363 | RRID:SCR_001799 | v1.4.5-unstable-66-4e44b43 |
| Software, algorithm | pindel | DOI:10.1093/bioinformatics/btp394 | RRID:SCR_000560 | v0.2.5b9, 20160729 |
| Software, algorithm | Tablet | DOI:10.1093/bib/bbs012 | RRID:SCR_000017 | v1.17.08.17 |
| Software, algorithm | samtools | DOI:10.1093/bioinformatics/btp352 | RRID:SCR_002105 | 1.9 |
| Software, algorithm | bwa | PMID:19451168 | RRID:SCR_010910 | 0.7.12-r1044 or later |
| Software, algorithm | picard | http://broadinstitute.github.io/picard/ | RRID:SCR_006525 | 1.110 or later |
| Software, algorithm | snpEff | PMID:22728672 | RRID:SCR_005191 | 4.1 g up to 4.3 t |
| Software, algorithm | R project for statistical computing | R Core Team | RRID:SCR_001905 | v3.4.4 |
| Software, algorithm | R package ggplot2 | H. Wickham | RRID:SCR_014601 | v3.2.1 |
| Software, algorithm | R package gridExtra | Baptiste Auguie (2017) | https://CRAN.R-project.org/package=gridExtra | v2.3 |
| Software, algorithm | R package igraph | Csardi G, Nepusz T | https://igraph.org/r/ | v1.1.1 |
| Software, algorithm | R package stats | R Development Core Team, 2015 | https://www.R-project.org/ | v3.4.4 |
| Software, algorithm | R package fmsb | Minato Nakazawa (2019) | https://CRAN.R-project.org/package=fmsb | v0.6.3 |
| Software, algorithm | R package plyr | Hadley Wickham (2011) | 10.18637/jss.v040.i01 | v1.8.4 |
| Software, algorithm | R package reshape2 | Hadley Wickham (2007) | 10.18637/jss.v021.i12 | v1.4.3 |
| Software, algorithm | R package GenomicFeatures | DOI:10.1371/journal.pcbi.1003118 | RRID:SCR_016960 | v1.30.3 |
| Software, algorithm | R package rtracklayer | DOI:10.1093/bioinformatics/btp328 | http://www.bioconductor.org/ | v1.38.3 |
| Software, algorithm | R Studio Desktop | RStudio Team (2020) | Version 1.0.143 |