Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (S. cerevisiae) | RDKY6677 | PMID:19641493 | uGCR wild-type | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6729 | PMID:19641493 | uGCR exo1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY8032 | PMID:24699249 | uGCR exo1Δ::TRP1 sgs1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9771 | This study | uGCR exo1Δ::HIS3 yku80Δ::kanMX4 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6686 | PMID:19641493 | uGCR mre11Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | HZY2771 | PMID:29505562 | uGCR cir0 mre11-H125N::TRP1 | Dr. Huilin Zhou (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6731 | PMID:19641493 | uGCR mus81Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6894 | PMID:24699249 | uGCR pif1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9773 | This study | uGCR pif1Δ::HIS3 yku80Δ::kanMX4 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6703 | PMID:19641493 | uGCR pol32Δ::TRP1 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6734 | PMID:19641493 | uGCR rad10Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6691 | PMID:19641493 | uGCR rad52Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6735 | PMID:19641493 | uGCR rrm3Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6687 | PMID:19641493 | uGCR sgs1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9445 | This study | uGCR sgs1Δ::HIS3 yku80Δ::kanMX4 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6738 | PMID:19641493 | uGCR slx1Δ::kanMX4 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6761 | PMID:19641493 | uGCR tel1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9506 | This study | uGCR yen1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY8006 | PMID:24699249 | uGCR yku80Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY6737 | PMID:24699249 | uGCR sae2Δ::TRP1 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9734 | This study | uGCR sae2Δ::TRP1 hotspotΔ | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9472 | This study | uGCR sae2-S267A | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9496 | This study | uGCR sae2-MT9 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY8020 | PMID:24699249 | uGCR sae2Δ::TRP1 exo1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9777 | This study | uGCR sae2Δ::TRP1 exo1Δ::HIS3
yku80Δ:kanMX4 |
Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9392 | This study | uGCR sae2Δ::kanMX4 mus81Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9447 | This study | uGCR sae2Δ::TRP1 pif1Δ::HIS3 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9779 | This study | uGCR sae2Δ::TRP1 pif1Δ::HIS3 yku80Δ::kanMX4 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9390 | This study | uGCR sae2Δ::kanMX4 pol32Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9123 | This study | uGCR sae2Δ::TRP1 rad10Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9504 | This study | uGCR sae2Δ::TRP1 rad52Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9125 | This study | uGCR sae2Δ::TRP1 rrm3Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9775 | This study | uGCR sae2Δ::TRP1 sgs1Δ::HIS3 yku80Δ::kanMX4 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9502 | This study | uGCR sae2Δ::TRP1 slx1Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY8018 | This study | uGCR sae2Δ::TRP1 tel1Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9500 | This study | uGCR sae2Δ::TRP1 yen1Δ::HIS3 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Strain, strain background (S. cerevisiae) | RDKY9443 | This study | uGCR sae2Δ::TRP1 yku80Δ::kanMX4 | Richard Kolodner (Ludwig Institute for Cancer Research) |
| Recombinant DNA reagent | bRA77 | PMID:28405019 | Dr. James Haber (Brandeis University) | |
| Recombinant DNA reagent | pRS425-Cas9-2XSapI | Dr. Bruce Futcher (State University of New York, Stoney Brook) | ||
| Recombinant DNA reagent | pRS315/sae2-MT9 | PMID:24699249 | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1923 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1924 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1929 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1938 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1939 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1940 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Recombinant DNA reagent | pRDK1941 | This study | Dr. Richard Kolodner (Ludwig Institute for Cancer Research) | |
| Sequence-based reagent | pRDK1923-top | This study | 5′-ATC AAT AGA TCA AAA TCC CCC CC-3′ | |
| Sequence-based reagent | pRDK1924-bottom | This study | 5′-AAC GGG GGG GAT TTT GAT CTA TT-3′ | |
| Sequence-based reagent | pRDK1924-top | This study | 5′-ATC TTG GCT CTG GTC AAT GAT TA-3′ | |
| Sequence-based reagent | pRDK1924-bottom | This study | 5′-AAC TAA TCA TTG ACC AGA GCC AA-3′ | |
| Sequence-based reagent | pRDK1924-top | This study | 5′-ATC TGA ACG CAT GAG AAA GCC CC-3′ | |
| Sequence-based reagent | pRDK1294-bottom | This study | 5′-AAC GGG GCT TTC TCA TGC GTT CA-3′ | |
| Sequence-based reagent | pRDK1929-top | This study | 5′-TCC GTG TTC CAT CCT ACA GAG TTT T-3′ | |
| Sequence-based reagent | pRDK1929-bottom | This study | 5′-TCT GTA GGA TGG AAC ACG GAG ATC A-3′ | |
| Sequence-based reagent | pRDK1938-top | This study | 5′-TTA CAT GTT CGA CCG TAC CCG TTT T-3′ | |
| Sequence-based reagent | pRDK1938-bottom | This study | 5′-GGG TAC GGT CGA ACA TGT AAG ATC A-3′ | |
| Sequence-based reagent | pRDK1939-top | This study | 5′-ATA CCT GGA CCC CAG GCA CCG TTT T-3′ | |
| Sequence-based reagent | pRDK1939-bottom | This study | 5′-GGT GCC TGG GGT CCA GGT ATG ATC A-3′ | |
| Sequence-based reagent | pRDK1940-top | This study | 5′-TCA AAT AGG CAT GAT CTT GTG TTT T-3′ | |
| Sequence-based reagent | pRDK1940-bottom | This study | 5′-ACA AGA TCA TGC CTA TTT GAG ATC A-3′ | |
| Sequence-based reagent | pRDK1941-top | This study | 5′-TCT TCC GGG GGC TTT TTT TTG TTT T-3′ | |
| Sequence-based reagent | pRDK1941-bottom | This study | 5′-AAA AAA AAG CCC CCG GAA GAG ATC A-3′ | |
| Sequence-based reagent | sae2-S267A repair fragment | This study | 5′-TGA TAA CTT GAG GAA TAG ATC AAA AGC GCC CCC AGG TTT TGG AAG ACT GGA TTT TCC CTC-3′ | |
| Sequence-based reagent | sae2-MT9 amplification forward primer | This study | 5′-TCC ACC ATT CGA GTC TTG AG-3′ | |
| Sequence-based reagent | sae2-MT9 amplification reverse primer | This study | 5′-TTC CCC TTT CTG CTT TAC CA-3′ | |
| Sequence-based reagent | hotspotΔ repair fragment | This study | 5′-TCA AGA ATT CAG ATC TTC CAG TGG TGC ATG AAC GCA TGA GGG CGC GCG ATA CAG ACC GGT TCA GAC AGG ATA AAG AGG AA-3′ | |
| Commercial assay or kit | Gentra Puregene Yeast/Bacteria Kit | Qiagen | 158567 | |
| Commercial assay or kit | TruSeq DNA PCR-free LT kit | Illumina | 15037158 | |
| Software, algorithm | Bowtie 2.2.1 | PMID:22388286 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| Software, algorithm | Pyrus 0.7 | PMID:24699249 | https://sourceforge.net/projects/pyrus-seq/ |