Recombinant:Article Title: The modifiers that cause changes in gene essentiality.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 antibody Abcam ab1791; RRID:AB_302613 Chemicals, peptides, and recombinant proteins L-Glutamic acid monosodium (MSG) Sigma-Aldrich Cat#G5889 L-Canavanine sulfate salt (CAN) Sigma-Aldrich Cat#C9758 S-(2-Aminoethyl)-L-cysteine hydrochloride (LYP) Sigma-Aldrich Cat#A2636 Hygromycin B (HYG) Formedium Cat#HYG0500 Nourseothricin (NAT) Jena Bioscience CatAB-102XL G-418 disulphate (G418) Formedium Cat#108321-42-2 5-Fluoroorotic acid monohydrate (5-FOA) Formedium Cat#5FOA10-10 α-factor mating pheromone ZymoResearch, Lucerna Chem Cat#Y1001 β-mercaptoethanol Gibco Cat#31350-010 Ponceau S PanReac/Applichem Cat#A1405.0100 Paraformaldehyde PanReac/Applichem Cat#211511.1211 K 2 HPO 4 for potassium phosphate buffer PanReac/Applichem Cat#A1042.1000 KH 2 PO 4 for potassium phosphate buffer PanReac/Applichem Cat#131509.1211 Sorbitol Applichem Cat#A2222.1000 Nitrocellulose filters Millipore Cat#AAWP02500 Trichloroacetic acid (TCA) PanReac/Applichem Cat#A1431.1000 Trichloroacetic acid (TCA) for dNTP measurements Sigma-Aldrich Cat#T6399 Dichloromethane Supelco, Merck Cat#1.06044 Trioctylamine Sigma-Aldrich Cat#T81000 Ammonium carbonate Fisher Chemical Cat#10785511 Affi-Gel Boronate Gel columns Bio-Rad Cat#1536103 Partisphere SAX column (125 mm × 4.6 mm, 5 μm) Hichrom Cat#HI-4621-0505 1 μCi/mL 35 S-methionine Revvity Cat#NEG709A500UC 25-mm Whatman glass fiber filters Supelco, Merck Cat#WHA1822025 Scintillation fluid (Ultima Gold F) Revvity Cat#6013171 Critical commercial assays DNeasy Blood & Tissue kit Qiagen Cat#69504 Deposited data SRA: PRNJA1131954 (whole-genome sequencing data) This paper https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA1131954 Dataset: Polymorphic genes Chen et al. 13 N/A Dataset: Background healthy genes Caudal et al. 12 N/A Dataset: Strain-specific genes Wang et al. 17 N/A Dataset: Dispensable essential genes Van Leeuwen et al. 20 N/A Dataset: 1,011 genomes project Peter et al. 25 http://1002genomes.u-strasbg.fr/files Dataset: Gene copy number and conservation Koch et al. 70 N/A Dataset: Expression level Lipson et al. 71 N/A Dataset: Expression variation under different environmental conditions Gasch et al. 72 N/A (Continued on next page) e1 Cell Systems 17, 101515, April 15, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dataset: MEFIT scores Huttenhower et al. 73 N/A Dataset: GO SLIM biological process annotations Ashburner et al. 74 N/A Dataset: Cocomplex degree Babu et al. 75 N/A Dataset: Protein complexes Meldal et al. 76 N/A Datasets: To define a core set of essential genes Van Leeuwen et al. 20 ; Chen et al. 13 ; Dowell et al. 8 N/A S288C reference genome version R64.2.1 SGD N/A Saccharomyces cerevisiae natural isolate genome sequences, see Data S10 Peter et al. 25 ; Duan et al. 77 See Data S10 Experimental models: Organisms/strains TS-allele-on-plasmid collection (MATα xxxΔ::KlLeu2_natR(Cterm) his3Δ1 leu2Δ0 ura3Δ0 [xxx-ts_natR(Nterm), AgSTE3prhphR, URA3] and MATa xxxΔ::natR_kanR(Cterm) his3Δ1 leu2Δ0 ura3Δ0 [xxx-ts_kanR(Nterm), AgMFA2prhphR, URA3]) Van Leeuwen et al. 20 See Data S9 BY4741 and BY4742 deletion mutant collections (MATa xxxΔ::kanMX4 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 and MATα xxxΔ::kanMX4 his3Δ1 leu2Δ0 ura3Δ0 lys2Δ0) Euroscarf See Data S9 All other yeast strains, see Data S9 See Data S9 See Data S9 Oligonucleotides Primers for amplifying genes from the wild genome, see Data S9 This paper N/A Primers for Sanger sequencing, see Data S9 This paper N/A Oligos for creating a dsDNA repair template for gene knockout, see Data S9 This paper N/A Recombinant DNA pML104 Laughery et al. 78 Addgene #67638 pML104-HygMX4 Patricia Wittkopp Addgene #83475 pML107 Laughery et al. 78 Addgene #67639 pML104-kanR1136 Parts et al. 24 Addgene #162040 pML107-kanR468 Parts et al. 24 Addgene #162041 pML104-natR412 Parts et al. 24 Addgene #162042 pML107-natR854 Parts et al. 24 Addgene #162043 pYES2-HTH (HIS10-TEV-HA (HTH) epitope tag) Singh et al. 50 Addgene #86470 pYES2-HTH-HHT2 Singh et al. 50 Addgene #86482 Plasmids expressing Cas9 and a gRNA, see Data S9 This paper N/A TS-allele-on-plasmid vectors, see Data S9 Van Leeuwen et al. 20 N/A All other plasmids, see Data S9 See Data S9 See Data S9 Software and algorithms Cell Profiler Carpenter et al. 79 https://cellprofiler.org ZEN Blue software Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html Fiji Schindelin et al. 80 https://imagej.net/software/fiji/downloads BWA v0.7.17 Li and Durbin 81 https://bio-bwa.sourceforge.net (Continued on next page) Cell Systems 17, 101515, April 15, 2026 e2
Sequencing:Article Title: The modifiers that cause changes in gene essentiality.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 antibody Abcam ab1791; RRID:AB_302613 Chemicals, peptides, and recombinant proteins L-Glutamic acid monosodium (MSG) Sigma-Aldrich Cat#G5889 L-Canavanine sulfate salt (CAN) Sigma-Aldrich Cat#C9758 S-(2-Aminoethyl)-L-cysteine hydrochloride (LYP) Sigma-Aldrich Cat#A2636 Hygromycin B (HYG) Formedium Cat#HYG0500 Nourseothricin (NAT) Jena Bioscience CatAB-102XL G-418 disulphate (G418) Formedium Cat#108321-42-2 5-Fluoroorotic acid monohydrate (5-FOA) Formedium Cat#5FOA10-10 α-factor mating pheromone ZymoResearch, Lucerna Chem Cat#Y1001 β-mercaptoethanol Gibco Cat#31350-010 Ponceau S PanReac/Applichem Cat#A1405.0100 Paraformaldehyde PanReac/Applichem Cat#211511.1211 K 2 HPO 4 for potassium phosphate buffer PanReac/Applichem Cat#A1042.1000 KH 2 PO 4 for potassium phosphate buffer PanReac/Applichem Cat#131509.1211 Sorbitol Applichem Cat#A2222.1000 Nitrocellulose filters Millipore Cat#AAWP02500 Trichloroacetic acid (TCA) PanReac/Applichem Cat#A1431.1000 Trichloroacetic acid (TCA) for dNTP measurements Sigma-Aldrich Cat#T6399 Dichloromethane Supelco, Merck Cat#1.06044 Trioctylamine Sigma-Aldrich Cat#T81000 Ammonium carbonate Fisher Chemical Cat#10785511 Affi-Gel Boronate Gel columns Bio-Rad Cat#1536103 Partisphere SAX column (125 mm × 4.6 mm, 5 μm) Hichrom Cat#HI-4621-0505 1 μCi/mL 35 S-methionine Revvity Cat#NEG709A500UC 25-mm Whatman glass fiber filters Supelco, Merck Cat#WHA1822025 Scintillation fluid (Ultima Gold F) Revvity Cat#6013171 Critical commercial assays DNeasy Blood & Tissue kit Qiagen Cat#69504 Deposited data SRA: PRNJA1131954 (whole-genome sequencing data) This paper https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA1131954 Dataset: Polymorphic genes Chen et al. 13 N/A Dataset: Background healthy genes Caudal et al. 12 N/A Dataset: Strain-specific genes Wang et al. 17 N/A Dataset: Dispensable essential genes Van Leeuwen et al. 20 N/A Dataset: 1,011 genomes project Peter et al. 25 http://1002genomes.u-strasbg.fr/files Dataset: Gene copy number and conservation Koch et al. 70 N/A Dataset: Expression level Lipson et al. 71 N/A Dataset: Expression variation under different environmental conditions Gasch et al. 72 N/A (Continued on next page) e1 Cell Systems 17, 101515, April 15, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dataset: MEFIT scores Huttenhower et al. 73 N/A Dataset: GO SLIM biological process annotations Ashburner et al. 74 N/A Dataset: Cocomplex degree Babu et al. 75 N/A Dataset: Protein complexes Meldal et al. 76 N/A Datasets: To define a core set of essential genes Van Leeuwen et al. 20 ; Chen et al. 13 ; Dowell et al. 8 N/A S288C reference genome version R64.2.1 SGD N/A Saccharomyces cerevisiae natural isolate genome sequences, see Data S10 Peter et al. 25 ; Duan et al. 77 See Data S10 Experimental models: Organisms/strains TS-allele-on-plasmid collection (MATα xxxΔ::KlLeu2_natR(Cterm) his3Δ1 leu2Δ0 ura3Δ0 [xxx-ts_natR(Nterm), AgSTE3prhphR, URA3] and MATa xxxΔ::natR_kanR(Cterm) his3Δ1 leu2Δ0 ura3Δ0 [xxx-ts_kanR(Nterm), AgMFA2prhphR, URA3]) Van Leeuwen et al. 20 See Data S9 BY4741 and BY4742 deletion mutant collections (MATa xxxΔ::kanMX4 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 and MATα xxxΔ::kanMX4 his3Δ1 leu2Δ0 ura3Δ0 lys2Δ0) Euroscarf See Data S9 All other yeast strains, see Data S9 See Data S9 See Data S9 Oligonucleotides Primers for amplifying genes from the wild genome, see Data S9 This paper N/A Primers for Sanger sequencing, see Data S9 This paper N/A Oligos for creating a dsDNA repair template for gene knockout, see Data S9 This paper N/A Recombinant DNA pML104 Laughery et al. 78 Addgene #67638 pML104-HygMX4 Patricia Wittkopp Addgene #83475 pML107 Laughery et al. 78 Addgene #67639 pML104-kanR1136 Parts et al. 24 Addgene #162040 pML107-kanR468 Parts et al. 24 Addgene #162041 pML104-natR412 Parts et al. 24 Addgene #162042 pML107-natR854 Parts et al. 24 Addgene #162043 pYES2-HTH (HIS10-TEV-HA (HTH) epitope tag) Singh et al. 50 Addgene #86470 pYES2-HTH-HHT2 Singh et al. 50 Addgene #86482 Plasmids expressing Cas9 and a gRNA, see Data S9 This paper N/A TS-allele-on-plasmid vectors, see Data S9 Van Leeuwen et al. 20 N/A All other plasmids, see Data S9 See Data S9 See Data S9 Software and algorithms Cell Profiler Carpenter et al. 79 https://cellprofiler.org ZEN Blue software Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html Fiji Schindelin et al. 80 https://imagej.net/software/fiji/downloads BWA v0.7.17 Li and Durbin 81 https://bio-bwa.sourceforge.net (Continued on next page) Cell Systems 17, 101515, April 15, 2026 e2
Expressing:Article Title: The modifiers that cause changes in gene essentiality.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Histone H3 antibody Abcam ab1791; RRID:AB_302613 Chemicals, peptides, and recombinant proteins L-Glutamic acid monosodium (MSG) Sigma-Aldrich Cat#G5889 L-Canavanine sulfate salt (CAN) Sigma-Aldrich Cat#C9758 S-(2-Aminoethyl)-L-cysteine hydrochloride (LYP) Sigma-Aldrich Cat#A2636 Hygromycin B (HYG) Formedium Cat#HYG0500 Nourseothricin (NAT) Jena Bioscience CatAB-102XL G-418 disulphate (G418) Formedium Cat#108321-42-2 5-Fluoroorotic acid monohydrate (5-FOA) Formedium Cat#5FOA10-10 α-factor mating pheromone ZymoResearch, Lucerna Chem Cat#Y1001 β-mercaptoethanol Gibco Cat#31350-010 Ponceau S PanReac/Applichem Cat#A1405.0100 Paraformaldehyde PanReac/Applichem Cat#211511.1211 K 2 HPO 4 for potassium phosphate buffer PanReac/Applichem Cat#A1042.1000 KH 2 PO 4 for potassium phosphate buffer PanReac/Applichem Cat#131509.1211 Sorbitol Applichem Cat#A2222.1000 Nitrocellulose filters Millipore Cat#AAWP02500 Trichloroacetic acid (TCA) PanReac/Applichem Cat#A1431.1000 Trichloroacetic acid (TCA) for dNTP measurements Sigma-Aldrich Cat#T6399 Dichloromethane Supelco, Merck Cat#1.06044 Trioctylamine Sigma-Aldrich Cat#T81000 Ammonium carbonate Fisher Chemical Cat#10785511 Affi-Gel Boronate Gel columns Bio-Rad Cat#1536103 Partisphere SAX column (125 mm × 4.6 mm, 5 μm) Hichrom Cat#HI-4621-0505 1 μCi/mL 35 S-methionine Revvity Cat#NEG709A500UC 25-mm Whatman glass fiber filters Supelco, Merck Cat#WHA1822025 Scintillation fluid (Ultima Gold F) Revvity Cat#6013171 Critical commercial assays DNeasy Blood & Tissue kit Qiagen Cat#69504 Deposited data SRA: PRNJA1131954 (whole-genome sequencing data) This paper https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA1131954 Dataset: Polymorphic genes Chen et al. 13 N/A Dataset: Background healthy genes Caudal et al. 12 N/A Dataset: Strain-specific genes Wang et al. 17 N/A Dataset: Dispensable essential genes Van Leeuwen et al. 20 N/A Dataset: 1,011 genomes project Peter et al. 25 http://1002genomes.u-strasbg.fr/files Dataset: Gene copy number and conservation Koch et al. 70 N/A Dataset: Expression level Lipson et al. 71 N/A Dataset: Expression variation under different environmental conditions Gasch et al. 72 N/A (Continued on next page) e1 Cell Systems 17, 101515, April 15, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dataset: MEFIT scores Huttenhower et al. 73 N/A Dataset: GO SLIM biological process annotations Ashburner et al. 74 N/A Dataset: Cocomplex degree Babu et al. 75 N/A Dataset: Protein complexes Meldal et al. 76 N/A Datasets: To define a core set of essential genes Van Leeuwen et al. 20 ; Chen et al. 13 ; Dowell et al. 8 N/A S288C reference genome version R64.2.1 SGD N/A Saccharomyces cerevisiae natural isolate genome sequences, see Data S10 Peter et al. 25 ; Duan et al. 77 See Data S10 Experimental models: Organisms/strains TS-allele-on-plasmid collection (MATα xxxΔ::KlLeu2_natR(Cterm) his3Δ1 leu2Δ0 ura3Δ0 [xxx-ts_natR(Nterm), AgSTE3prhphR, URA3] and MATa xxxΔ::natR_kanR(Cterm) his3Δ1 leu2Δ0 ura3Δ0 [xxx-ts_kanR(Nterm), AgMFA2prhphR, URA3]) Van Leeuwen et al. 20 See Data S9 BY4741 and BY4742 deletion mutant collections (MATa xxxΔ::kanMX4 his3Δ1 leu2Δ0 ura3Δ0 met15Δ0 and MATα xxxΔ::kanMX4 his3Δ1 leu2Δ0 ura3Δ0 lys2Δ0) Euroscarf See Data S9 All other yeast strains, see Data S9 See Data S9 See Data S9 Oligonucleotides Primers for amplifying genes from the wild genome, see Data S9 This paper N/A Primers for Sanger sequencing, see Data S9 This paper N/A Oligos for creating a dsDNA repair template for gene knockout, see Data S9 This paper N/A Recombinant DNA pML104 Laughery et al. 78 Addgene #67638 pML104-HygMX4 Patricia Wittkopp Addgene #83475 pML107 Laughery et al. 78 Addgene #67639 pML104-kanR1136 Parts et al. 24 Addgene #162040 pML107-kanR468 Parts et al. 24 Addgene #162041 pML104-natR412 Parts et al. 24 Addgene #162042 pML107-natR854 Parts et al. 24 Addgene #162043 pYES2-HTH (HIS10-TEV-HA (HTH) epitope tag) Singh et al. 50 Addgene #86470 pYES2-HTH-HHT2 Singh et al. 50 Addgene #86482 Plasmids expressing Cas9 and a gRNA, see Data S9 This paper N/A TS-allele-on-plasmid vectors, see Data S9 Van Leeuwen et al. 20 N/A All other plasmids, see Data S9 See Data S9 See Data S9 Software and algorithms Cell Profiler Carpenter et al. 79 https://cellprofiler.org ZEN Blue software Zeiss https://www.zeiss.com/microscopy/en/ products/software/zeiss-zen.html Fiji Schindelin et al. 80 https://imagej.net/software/fiji/downloads BWA v0.7.17 Li and Durbin 81 https://bio-bwa.sourceforge.net (Continued on next page) Cell Systems 17, 101515, April 15, 2026 e2
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