Virus:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Article Title: Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Capnocytophaga gingivalis strain DSM 3290 Leibniz Institute DSMZ (Braunschweig, Germany) DSM 3290-0522-001 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Scientific Cat# 10131-035 docetaxel MedChem Express Cat# HY-B0011 paclitaxel MedChem Express Cat# HY-B0015 5-FU MedChem Express Cat# HY-90006 cisplatin MedChem Express Cat# HY-17394 oxaliplatin MedChem Express Cat# HY-17371 trypsin Thermo Fisher Scientific Cat# 25300054 Critical commercial assays WST-1 cell proliferation assay Roche Applied Science Cat# 50-100-3295 Universal SYBR Green One-Step Kit Bio-Rad Laboratories Cat# 1725151 Quick-DNA Miniprep Zymo Research Cat# D3024 Experimental models: Cell lines EBV-positive AGS Rona Scott Lab from Louisiana State University N/A EBV-negative AGS Rona Scott Lab from Louisiana State University N/A Cal27 ATCC CRL-2095 FaDu ATCC HTB-43 Software and algorithms R version 4.2.0 R Core Team https://www.R-project.org/ PERMANOVA (v2.6-4) N/A https://cran.r-project.org/web/ packages/PERMANOVA/index.html DESeq2 (1.50.2) N/A https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ALDEx2 (1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ALDEx2.html phyloseq (v1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/phyloseq.html ANCOMBC(v2.12.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ANCOMBC.html ggraph (v2.1.0) N/A https://cran.r-project.org/web/ packages/ggraph/index.html variancePartition (v1.28.9) N/A https://www.bioconductor.org/packages/ release/bioc/html/variancePartition.html MSigDB (v7.5.1) N/A https://igordot.github.io/msigdbr/ fgsea (v1.24.0) N/A https://bioconductor.org/packages/ release/bioc/html/fgsea.html BayesPrism (v2.2.2) N/A https://github.com/Danko-Lab/BayesPrism survival (v3.3-1) N/A https://cran.r-project.org/web/ packages/survival/index.html (Continued on next page) e1 Cell Reports Medicine 7, 102757, May 19, 2026 Article ll OPEN ACCESS ..
Article Title: Directed evolution of APOX for proximity labeling using phenols with high redox potentials.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken α-c-Myc MilliporeSigma Cat#AB3252 Goat AlexaFluor647-αCh ThermoFisher Cat#A-21449 Streptavidin-Phycoerythrin (SA-PE) ThermoFisher Cat#S886 Streptavidin-AlexaFluor568 (SA-A568) ThermoFisher Cat#S11226 Streptavidin-HRP (SA-HRP) ThermoFisher Cat#S911 Rabbit-αFlag Sigma Cat#F7425 Goat AlexaFluor488-αRabbit ThermoFisher Cat#A11008 mouse anti-BSA Sigma Cat#SAB4200688-100UL goat anti-mouse HRP conjugate Sigma Cat#AP124P Streptavidin-AlexaFluor594 (SA-A594) Invitrogen Cat#S11227 Bacterial and virus strains DH5α E.coli Invitrogen Cat#12034013 Saccharomyces cerevisiae strain BJ5465 ATCC Cat#208289 Biological samples Cortical neuronal cultures from prenatal Sprague-Dawley rats Envigo https://www.inotiv.com/hubfs/resources/ data-sheets/envigo-44-sprague-dawleymodel-sheet-cardiology-a4_screen.pdf Chemicals, peptides, and recombinant proteins Biotin-PEG3-azide ThermoFisher Cat#50-210-7600 Desthiobiotin-PEG3-azide Sigma Cat#902020 200 μL PierceTM Streptavidin Agarose beads Thermo Cat#20349 Carbonic anhydrase from bovine erythrocytes Sigma Cat#C3934-100MG Horseradish peroxidase Biosynth Cat#FP159434 phenosafranin Sigma Cat#199648-1G Nile blue Sigma Cat#370088 Critical commercial assays Zymoprep Yeast Plasmid Miniprep II Kit Zymo Research CatD2004 Deposited data mass spectrometry proteomics data ProteomeXchange Consortium via the PRIDE partner repository PXD060753 and 10.6019/PXD060753 https://www.ebi.ac.uk/pride/archive/ projects/PXD060753 Experimental models: Cell lines HEK 293 T ATCC CRL-3216 Recombinant DNA FUGW 3rd generation lentiviral plasmid Lois et al.81 Addgene plasmid #14883 Oligonucleotides Con2.Fwd (5′-CTAGTGGTGGAGGAGGCTCTGG TGGAGGCGGTAGCGGAGGCGGAGGGTCGGCTAG-3′) Integrated DNA Technologies N/A Con2.Rev (5′-TATCAGATCTCGAGCTATTACAAGTCCT CTTCAGAAATAAGCTTTTGTTCGGATCC-3′) Integrated DNA Technologies N/A HomR.Fwd (5′-CAAGGTCTGCAGGCTAGTGG TGGAGGAGGCTCTGGTG-3′) Integrated DNA Technologies N/A HomR.Rev (5′-CTACACTGTTGTTATCAGATC TCGAGCTATTACAAGTC-3′) Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Technology e1 Cell Chemical Biology 33, 1–15.e1–e13, April 16, 2026 .. HEK 293 T cells from ATCC (CRL-3216, passage number < 25, female origin, authenticated using STR profiling and mycoplasma testing) were cultured as a monolayer in DMEM (ATCC) supplemented with 10% (v/v) FBS (Corning) and 2 mM L-glutamine (ATCC) (DMEM-FBS) at 37 ◦C under 5% CO2.
Recombinant:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Article Title: Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Capnocytophaga gingivalis strain DSM 3290 Leibniz Institute DSMZ (Braunschweig, Germany) DSM 3290-0522-001 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Scientific Cat# 10131-035 docetaxel MedChem Express Cat# HY-B0011 paclitaxel MedChem Express Cat# HY-B0015 5-FU MedChem Express Cat# HY-90006 cisplatin MedChem Express Cat# HY-17394 oxaliplatin MedChem Express Cat# HY-17371 trypsin Thermo Fisher Scientific Cat# 25300054 Critical commercial assays WST-1 cell proliferation assay Roche Applied Science Cat# 50-100-3295 Universal SYBR Green One-Step Kit Bio-Rad Laboratories Cat# 1725151 Quick-DNA Miniprep Zymo Research Cat# D3024 Experimental models: Cell lines EBV-positive AGS Rona Scott Lab from Louisiana State University N/A EBV-negative AGS Rona Scott Lab from Louisiana State University N/A Cal27 ATCC CRL-2095 FaDu ATCC HTB-43 Software and algorithms R version 4.2.0 R Core Team https://www.R-project.org/ PERMANOVA (v2.6-4) N/A https://cran.r-project.org/web/ packages/PERMANOVA/index.html DESeq2 (1.50.2) N/A https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ALDEx2 (1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ALDEx2.html phyloseq (v1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/phyloseq.html ANCOMBC(v2.12.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ANCOMBC.html ggraph (v2.1.0) N/A https://cran.r-project.org/web/ packages/ggraph/index.html variancePartition (v1.28.9) N/A https://www.bioconductor.org/packages/ release/bioc/html/variancePartition.html MSigDB (v7.5.1) N/A https://igordot.github.io/msigdbr/ fgsea (v1.24.0) N/A https://bioconductor.org/packages/ release/bioc/html/fgsea.html BayesPrism (v2.2.2) N/A https://github.com/Danko-Lab/BayesPrism survival (v3.3-1) N/A https://cran.r-project.org/web/ packages/survival/index.html (Continued on next page) e1 Cell Reports Medicine 7, 102757, May 19, 2026 Article ll OPEN ACCESS ..
Article Title: Directed evolution of APOX for proximity labeling using phenols with high redox potentials.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken α-c-Myc MilliporeSigma Cat#AB3252 Goat AlexaFluor647-αCh ThermoFisher Cat#A-21449 Streptavidin-Phycoerythrin (SA-PE) ThermoFisher Cat#S886 Streptavidin-AlexaFluor568 (SA-A568) ThermoFisher Cat#S11226 Streptavidin-HRP (SA-HRP) ThermoFisher Cat#S911 Rabbit-αFlag Sigma Cat#F7425 Goat AlexaFluor488-αRabbit ThermoFisher Cat#A11008 mouse anti-BSA Sigma Cat#SAB4200688-100UL goat anti-mouse HRP conjugate Sigma Cat#AP124P Streptavidin-AlexaFluor594 (SA-A594) Invitrogen Cat#S11227 Bacterial and virus strains DH5α E.coli Invitrogen Cat#12034013 Saccharomyces cerevisiae strain BJ5465 ATCC Cat#208289 Biological samples Cortical neuronal cultures from prenatal Sprague-Dawley rats Envigo https://www.inotiv.com/hubfs/resources/ data-sheets/envigo-44-sprague-dawleymodel-sheet-cardiology-a4_screen.pdf Chemicals, peptides, and recombinant proteins Biotin-PEG3-azide ThermoFisher Cat#50-210-7600 Desthiobiotin-PEG3-azide Sigma Cat#902020 200 μL PierceTM Streptavidin Agarose beads Thermo Cat#20349 Carbonic anhydrase from bovine erythrocytes Sigma Cat#C3934-100MG Horseradish peroxidase Biosynth Cat#FP159434 phenosafranin Sigma Cat#199648-1G Nile blue Sigma Cat#370088 Critical commercial assays Zymoprep Yeast Plasmid Miniprep II Kit Zymo Research CatD2004 Deposited data mass spectrometry proteomics data ProteomeXchange Consortium via the PRIDE partner repository PXD060753 and 10.6019/PXD060753 https://www.ebi.ac.uk/pride/archive/ projects/PXD060753 Experimental models: Cell lines HEK 293 T ATCC CRL-3216 Recombinant DNA FUGW 3rd generation lentiviral plasmid Lois et al.81 Addgene plasmid #14883 Oligonucleotides Con2.Fwd (5′-CTAGTGGTGGAGGAGGCTCTGG TGGAGGCGGTAGCGGAGGCGGAGGGTCGGCTAG-3′) Integrated DNA Technologies N/A Con2.Rev (5′-TATCAGATCTCGAGCTATTACAAGTCCT CTTCAGAAATAAGCTTTTGTTCGGATCC-3′) Integrated DNA Technologies N/A HomR.Fwd (5′-CAAGGTCTGCAGGCTAGTGG TGGAGGAGGCTCTGGTG-3′) Integrated DNA Technologies N/A HomR.Rev (5′-CTACACTGTTGTTATCAGATC TCGAGCTATTACAAGTC-3′) Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Technology e1 Cell Chemical Biology 33, 1–15.e1–e13, April 16, 2026 .. HEK 293 T cells from ATCC (CRL-3216, passage number < 25, female origin, authenticated using STR profiling and mycoplasma testing) were cultured as a monolayer in DMEM (ATCC) supplemented with 10% (v/v) FBS (Corning) and 2 mM L-glutamine (ATCC) (DMEM-FBS) at 37 ◦C under 5% CO2.
Mutagenesis:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Software:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Article Title: Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Capnocytophaga gingivalis strain DSM 3290 Leibniz Institute DSMZ (Braunschweig, Germany) DSM 3290-0522-001 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Scientific Cat# 10131-035 docetaxel MedChem Express Cat# HY-B0011 paclitaxel MedChem Express Cat# HY-B0015 5-FU MedChem Express Cat# HY-90006 cisplatin MedChem Express Cat# HY-17394 oxaliplatin MedChem Express Cat# HY-17371 trypsin Thermo Fisher Scientific Cat# 25300054 Critical commercial assays WST-1 cell proliferation assay Roche Applied Science Cat# 50-100-3295 Universal SYBR Green One-Step Kit Bio-Rad Laboratories Cat# 1725151 Quick-DNA Miniprep Zymo Research Cat# D3024 Experimental models: Cell lines EBV-positive AGS Rona Scott Lab from Louisiana State University N/A EBV-negative AGS Rona Scott Lab from Louisiana State University N/A Cal27 ATCC CRL-2095 FaDu ATCC HTB-43 Software and algorithms R version 4.2.0 R Core Team https://www.R-project.org/ PERMANOVA (v2.6-4) N/A https://cran.r-project.org/web/ packages/PERMANOVA/index.html DESeq2 (1.50.2) N/A https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ALDEx2 (1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ALDEx2.html phyloseq (v1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/phyloseq.html ANCOMBC(v2.12.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ANCOMBC.html ggraph (v2.1.0) N/A https://cran.r-project.org/web/ packages/ggraph/index.html variancePartition (v1.28.9) N/A https://www.bioconductor.org/packages/ release/bioc/html/variancePartition.html MSigDB (v7.5.1) N/A https://igordot.github.io/msigdbr/ fgsea (v1.24.0) N/A https://bioconductor.org/packages/ release/bioc/html/fgsea.html BayesPrism (v2.2.2) N/A https://github.com/Danko-Lab/BayesPrism survival (v3.3-1) N/A https://cran.r-project.org/web/ packages/survival/index.html (Continued on next page) e1 Cell Reports Medicine 7, 102757, May 19, 2026 Article ll OPEN ACCESS ..
Construct:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Selection:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Marker:Article Title: Mechanistic modeling of recessive disease through allelic integration of variant effects.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains DH5α Competent Cells New England Biolabs Cat# C2987 Chemicals, peptides, and recombinant proteins Zymolyase 20T Zymo Research Cat# E1005 Doxycycline Hyclate APExBIO Cat# A4052 Deposited data NextSeq 2000 and Sequel II data This study GEO:GSE313314 Fitness scores and estimated enzyme activities This study MaveDB:urn:mavedb:00001257-a; MaveDB:urn:mavedb:00001257-0 Experimental models: Organisms/strains Saccharomyces cerevisiae: yTHC Parental Strain Horizon Discovery Cat# YSC1210 Saccharomyces cerevisiae: yTHC ADE13 Strain Horizon Discovery Source ID: TH_2644 Oligonucleotides Primers for saturation mutagenesis and PCRs Integrated DNA Technologies (IDT) N/A Recombinant DNA ADSL cDNA (yeast codon-optimized) Integrated DNA Technologies (IDT) N/A pMP1_xSADSL This study N/A pMP1_xLADSL This study N/A pAINt_ADSL This study N/A Software and algorithms Trimmomatic PMID: 24695404 RRID:SCR_011848 alignparse PMID: 31897449 GitHub:https://github.com/jbloomlab/alignparse SSDraw PMID: 37786684 GitHub:https://github.com/ncbi/SSDraw Enrich2 PMID: 28784151 RRID:SCR_019241 ChimeraX PMID: 32881101 RRID:SCR_015872 Python 3 Python Software Foundation RRID:SCR_008394 Scripts and code This study Zenodo:https://doi.org/10.5281/zenodo.17832781 Other Illumina NextSeq 2000 Illumina N/A PacBio Sequel II Pacific Biosciences N/A Infinite M200 Pro Tecan N/A 96-Well Plates Greiner CELLSTAR Cat# M1062-40EA ll OPEN ACCESSArticle Cell Systems 17, 101595, June 17, 2026 e1 For transformations, synthetic complete medium lacking histidine (SC-His) was used to select positive transformants, as constructs were integrated using a histidine selection marker. ..
Proliferation Assay:Article Title: Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Capnocytophaga gingivalis strain DSM 3290 Leibniz Institute DSMZ (Braunschweig, Germany) DSM 3290-0522-001 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Scientific Cat# 10131-035 docetaxel MedChem Express Cat# HY-B0011 paclitaxel MedChem Express Cat# HY-B0015 5-FU MedChem Express Cat# HY-90006 cisplatin MedChem Express Cat# HY-17394 oxaliplatin MedChem Express Cat# HY-17371 trypsin Thermo Fisher Scientific Cat# 25300054 Critical commercial assays WST-1 cell proliferation assay Roche Applied Science Cat# 50-100-3295 Universal SYBR Green One-Step Kit Bio-Rad Laboratories Cat# 1725151 Quick-DNA Miniprep Zymo Research Cat# D3024 Experimental models: Cell lines EBV-positive AGS Rona Scott Lab from Louisiana State University N/A EBV-negative AGS Rona Scott Lab from Louisiana State University N/A Cal27 ATCC CRL-2095 FaDu ATCC HTB-43 Software and algorithms R version 4.2.0 R Core Team https://www.R-project.org/ PERMANOVA (v2.6-4) N/A https://cran.r-project.org/web/ packages/PERMANOVA/index.html DESeq2 (1.50.2) N/A https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ALDEx2 (1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ALDEx2.html phyloseq (v1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/phyloseq.html ANCOMBC(v2.12.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ANCOMBC.html ggraph (v2.1.0) N/A https://cran.r-project.org/web/ packages/ggraph/index.html variancePartition (v1.28.9) N/A https://www.bioconductor.org/packages/ release/bioc/html/variancePartition.html MSigDB (v7.5.1) N/A https://igordot.github.io/msigdbr/ fgsea (v1.24.0) N/A https://bioconductor.org/packages/ release/bioc/html/fgsea.html BayesPrism (v2.2.2) N/A https://github.com/Danko-Lab/BayesPrism survival (v3.3-1) N/A https://cran.r-project.org/web/ packages/survival/index.html (Continued on next page) e1 Cell Reports Medicine 7, 102757, May 19, 2026 Article ll OPEN ACCESS ..
SYBR Green Assay:Article Title: Sex-biased intratumoral microbiome influences tumor molecular and immune landscape and disease outcomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Capnocytophaga gingivalis strain DSM 3290 Leibniz Institute DSMZ (Braunschweig, Germany) DSM 3290-0522-001 Chemicals, peptides, and recombinant proteins G418 Thermo Fisher Scientific Cat# 10131-035 docetaxel MedChem Express Cat# HY-B0011 paclitaxel MedChem Express Cat# HY-B0015 5-FU MedChem Express Cat# HY-90006 cisplatin MedChem Express Cat# HY-17394 oxaliplatin MedChem Express Cat# HY-17371 trypsin Thermo Fisher Scientific Cat# 25300054 Critical commercial assays WST-1 cell proliferation assay Roche Applied Science Cat# 50-100-3295 Universal SYBR Green One-Step Kit Bio-Rad Laboratories Cat# 1725151 Quick-DNA Miniprep Zymo Research Cat# D3024 Experimental models: Cell lines EBV-positive AGS Rona Scott Lab from Louisiana State University N/A EBV-negative AGS Rona Scott Lab from Louisiana State University N/A Cal27 ATCC CRL-2095 FaDu ATCC HTB-43 Software and algorithms R version 4.2.0 R Core Team https://www.R-project.org/ PERMANOVA (v2.6-4) N/A https://cran.r-project.org/web/ packages/PERMANOVA/index.html DESeq2 (1.50.2) N/A https://bioconductor.org/packages/ release/bioc/html/DESeq2.html ALDEx2 (1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ALDEx2.html phyloseq (v1.42.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/phyloseq.html ANCOMBC(v2.12.0) N/A https://www.bioconductor.org/packages/ release/bioc/html/ANCOMBC.html ggraph (v2.1.0) N/A https://cran.r-project.org/web/ packages/ggraph/index.html variancePartition (v1.28.9) N/A https://www.bioconductor.org/packages/ release/bioc/html/variancePartition.html MSigDB (v7.5.1) N/A https://igordot.github.io/msigdbr/ fgsea (v1.24.0) N/A https://bioconductor.org/packages/ release/bioc/html/fgsea.html BayesPrism (v2.2.2) N/A https://github.com/Danko-Lab/BayesPrism survival (v3.3-1) N/A https://cran.r-project.org/web/ packages/survival/index.html (Continued on next page) e1 Cell Reports Medicine 7, 102757, May 19, 2026 Article ll OPEN ACCESS ..
Plasmid Preparation:Article Title: Directed evolution of APOX for proximity labeling using phenols with high redox potentials.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken α-c-Myc MilliporeSigma Cat#AB3252 Goat AlexaFluor647-αCh ThermoFisher Cat#A-21449 Streptavidin-Phycoerythrin (SA-PE) ThermoFisher Cat#S886 Streptavidin-AlexaFluor568 (SA-A568) ThermoFisher Cat#S11226 Streptavidin-HRP (SA-HRP) ThermoFisher Cat#S911 Rabbit-αFlag Sigma Cat#F7425 Goat AlexaFluor488-αRabbit ThermoFisher Cat#A11008 mouse anti-BSA Sigma Cat#SAB4200688-100UL goat anti-mouse HRP conjugate Sigma Cat#AP124P Streptavidin-AlexaFluor594 (SA-A594) Invitrogen Cat#S11227 Bacterial and virus strains DH5α E.coli Invitrogen Cat#12034013 Saccharomyces cerevisiae strain BJ5465 ATCC Cat#208289 Biological samples Cortical neuronal cultures from prenatal Sprague-Dawley rats Envigo https://www.inotiv.com/hubfs/resources/ data-sheets/envigo-44-sprague-dawleymodel-sheet-cardiology-a4_screen.pdf Chemicals, peptides, and recombinant proteins Biotin-PEG3-azide ThermoFisher Cat#50-210-7600 Desthiobiotin-PEG3-azide Sigma Cat#902020 200 μL PierceTM Streptavidin Agarose beads Thermo Cat#20349 Carbonic anhydrase from bovine erythrocytes Sigma Cat#C3934-100MG Horseradish peroxidase Biosynth Cat#FP159434 phenosafranin Sigma Cat#199648-1G Nile blue Sigma Cat#370088 Critical commercial assays Zymoprep Yeast Plasmid Miniprep II Kit Zymo Research CatD2004 Deposited data mass spectrometry proteomics data ProteomeXchange Consortium via the PRIDE partner repository PXD060753 and 10.6019/PXD060753 https://www.ebi.ac.uk/pride/archive/ projects/PXD060753 Experimental models: Cell lines HEK 293 T ATCC CRL-3216 Recombinant DNA FUGW 3rd generation lentiviral plasmid Lois et al.81 Addgene plasmid #14883 Oligonucleotides Con2.Fwd (5′-CTAGTGGTGGAGGAGGCTCTGG TGGAGGCGGTAGCGGAGGCGGAGGGTCGGCTAG-3′) Integrated DNA Technologies N/A Con2.Rev (5′-TATCAGATCTCGAGCTATTACAAGTCCT CTTCAGAAATAAGCTTTTGTTCGGATCC-3′) Integrated DNA Technologies N/A HomR.Fwd (5′-CAAGGTCTGCAGGCTAGTGG TGGAGGAGGCTCTGGTG-3′) Integrated DNA Technologies N/A HomR.Rev (5′-CTACACTGTTGTTATCAGATC TCGAGCTATTACAAGTC-3′) Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Technology e1 Cell Chemical Biology 33, 1–15.e1–e13, April 16, 2026 .. HEK 293 T cells from ATCC (CRL-3216, passage number < 25, female origin, authenticated using STR profiling and mycoplasma testing) were cultured as a monolayer in DMEM (ATCC) supplemented with 10% (v/v) FBS (Corning) and 2 mM L-glutamine (ATCC) (DMEM-FBS) at 37 ◦C under 5% CO2.
Mass Spectrometry:Article Title: Directed evolution of APOX for proximity labeling using phenols with high redox potentials.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Chicken α-c-Myc MilliporeSigma Cat#AB3252 Goat AlexaFluor647-αCh ThermoFisher Cat#A-21449 Streptavidin-Phycoerythrin (SA-PE) ThermoFisher Cat#S886 Streptavidin-AlexaFluor568 (SA-A568) ThermoFisher Cat#S11226 Streptavidin-HRP (SA-HRP) ThermoFisher Cat#S911 Rabbit-αFlag Sigma Cat#F7425 Goat AlexaFluor488-αRabbit ThermoFisher Cat#A11008 mouse anti-BSA Sigma Cat#SAB4200688-100UL goat anti-mouse HRP conjugate Sigma Cat#AP124P Streptavidin-AlexaFluor594 (SA-A594) Invitrogen Cat#S11227 Bacterial and virus strains DH5α E.coli Invitrogen Cat#12034013 Saccharomyces cerevisiae strain BJ5465 ATCC Cat#208289 Biological samples Cortical neuronal cultures from prenatal Sprague-Dawley rats Envigo https://www.inotiv.com/hubfs/resources/ data-sheets/envigo-44-sprague-dawleymodel-sheet-cardiology-a4_screen.pdf Chemicals, peptides, and recombinant proteins Biotin-PEG3-azide ThermoFisher Cat#50-210-7600 Desthiobiotin-PEG3-azide Sigma Cat#902020 200 μL PierceTM Streptavidin Agarose beads Thermo Cat#20349 Carbonic anhydrase from bovine erythrocytes Sigma Cat#C3934-100MG Horseradish peroxidase Biosynth Cat#FP159434 phenosafranin Sigma Cat#199648-1G Nile blue Sigma Cat#370088 Critical commercial assays Zymoprep Yeast Plasmid Miniprep II Kit Zymo Research CatD2004 Deposited data mass spectrometry proteomics data ProteomeXchange Consortium via the PRIDE partner repository PXD060753 and 10.6019/PXD060753 https://www.ebi.ac.uk/pride/archive/ projects/PXD060753 Experimental models: Cell lines HEK 293 T ATCC CRL-3216 Recombinant DNA FUGW 3rd generation lentiviral plasmid Lois et al.81 Addgene plasmid #14883 Oligonucleotides Con2.Fwd (5′-CTAGTGGTGGAGGAGGCTCTGG TGGAGGCGGTAGCGGAGGCGGAGGGTCGGCTAG-3′) Integrated DNA Technologies N/A Con2.Rev (5′-TATCAGATCTCGAGCTATTACAAGTCCT CTTCAGAAATAAGCTTTTGTTCGGATCC-3′) Integrated DNA Technologies N/A HomR.Fwd (5′-CAAGGTCTGCAGGCTAGTGG TGGAGGAGGCTCTGGTG-3′) Integrated DNA Technologies N/A HomR.Rev (5′-CTACACTGTTGTTATCAGATC TCGAGCTATTACAAGTC-3′) Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Technology e1 Cell Chemical Biology 33, 1–15.e1–e13, April 16, 2026 .. HEK 293 T cells from ATCC (CRL-3216, passage number < 25, female origin, authenticated using STR profiling and mycoplasma testing) were cultured as a monolayer in DMEM (ATCC) supplemented with 10% (v/v) FBS (Corning) and 2 mM L-glutamine (ATCC) (DMEM-FBS) at 37 ◦C under 5% CO2.
Polymerase Chain Reaction:Article Title: Exosomal microRNAs from Alveolar Macrophages Reveal a Protective Role of the Lung Microbiome Against Oncogenic Signaling During PAH Exposure
Article Snippet: To prepare the library, the NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA, USA) was used with ~5 ng of total RNA determined by the Bioanalyzer RNA 6000 Pico Kit (Agilent, Santa Clara, CA, USA) in a 5 μL solution as input, following the manufacturer’s protocol except for a modification of library size selection to increase small RNA detection sensitivity and specificity. .. After 15 cycles of PCR for indexing and library enrichment, an equal volume of 10 μL PCR mix (library without size selection) per sample together with the same volume of the negative control were pooled, followed by DNA cleanup using DNA Clean & Concentrator (Zymo Research, Irvine, CA, USA) and mixed with 135 and 319 bp custom-made ladders targeting the library’s 16–24 miRNA cDNA insert. .. Next, precise size selection of the 135–319 bp library via 2.75% agarose gel electrophoresis was performed, and library concentration was measured by qPCR using the NEBNext Library Quant Kit (New England BioLabs) on a QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific).
Size Selection:Article Title: Exosomal microRNAs from Alveolar Macrophages Reveal a Protective Role of the Lung Microbiome Against Oncogenic Signaling During PAH Exposure
Article Snippet: To prepare the library, the NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA, USA) was used with ~5 ng of total RNA determined by the Bioanalyzer RNA 6000 Pico Kit (Agilent, Santa Clara, CA, USA) in a 5 μL solution as input, following the manufacturer’s protocol except for a modification of library size selection to increase small RNA detection sensitivity and specificity. .. After 15 cycles of PCR for indexing and library enrichment, an equal volume of 10 μL PCR mix (library without size selection) per sample together with the same volume of the negative control were pooled, followed by DNA cleanup using DNA Clean & Concentrator (Zymo Research, Irvine, CA, USA) and mixed with 135 and 319 bp custom-made ladders targeting the library’s 16–24 miRNA cDNA insert. .. Next, precise size selection of the 135–319 bp library via 2.75% agarose gel electrophoresis was performed, and library concentration was measured by qPCR using the NEBNext Library Quant Kit (New England BioLabs) on a QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific).
Negative Control:Article Title: Exosomal microRNAs from Alveolar Macrophages Reveal a Protective Role of the Lung Microbiome Against Oncogenic Signaling During PAH Exposure
Article Snippet: To prepare the library, the NEBNext small RNA sample library preparation kit (New England BioLabs, Ipswich, MA, USA) was used with ~5 ng of total RNA determined by the Bioanalyzer RNA 6000 Pico Kit (Agilent, Santa Clara, CA, USA) in a 5 μL solution as input, following the manufacturer’s protocol except for a modification of library size selection to increase small RNA detection sensitivity and specificity. .. After 15 cycles of PCR for indexing and library enrichment, an equal volume of 10 μL PCR mix (library without size selection) per sample together with the same volume of the negative control were pooled, followed by DNA cleanup using DNA Clean & Concentrator (Zymo Research, Irvine, CA, USA) and mixed with 135 and 319 bp custom-made ladders targeting the library’s 16–24 miRNA cDNA insert. .. Next, precise size selection of the 135–319 bp library via 2.75% agarose gel electrophoresis was performed, and library concentration was measured by qPCR using the NEBNext Library Quant Kit (New England BioLabs) on a QuantStudio 5 Real-Time PCR System (Thermo Fisher Scientific).
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