Recombinant:Article Title: RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
Article Snippet: MS-5 mouse cells DSMZ ACC 441 .. Oligonucleotides Oligonucleotide sequences used in this study are provided in Table S9 This study N/A Recombinant DNA pcDNA5/FRT/TO-RNF25-WT-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRWD-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRING-mVenus3XFlag This study N/A pcDNA5/FRT/TO-mVenus-3xFlagGateway Di Fiore and Pines80 Addgene Plasmid #40999 pOG44_FLP_recombinase Hallacli et al.81 Addgene Plasmid #209087 Genome-wide All-in-One Brunello lentiviral library Doench et al.82 Addgene pooled library #73179 pX330-Puro Pritchard et al.83 Addgene Plasmid #82580 pU6-tevopreq1-GG-acceptor vector Nelson et al.84 Addgene Plasmid #174038 pU6-pegRNA-GG-acceptor vector Anzalone et al.85 Addgene Plasmid #132777 pCMV-PEmax Chen et al.86 Addgene Plasmid #174820 pEF1a-hMLH1dn Chen et al.86 Addgene Plasmid #174824 lentiGuide-Puro Sanjana et al.87 Addgene Plasmid #52963 pMDLg/pRRE Dull et al.88 Addgene Plasmid #12251 pRSV-Rev Dull et al.88 Addgene Plasmid #12253 pMD2.G/pVSV-g Didier Trono Addgene Plasmid #12259 Software and algorithms ImageLab (Version 5.2) Bio-Rad RRID:SCR_014210 SparkControl 3.1 Tecan https://lifesciences.tecan.com/multimode- plate-reader?p=tab–3 R (version 4.3.2) R Project for Statistical Computing RRID:SCR_001905 GraphPad Prism (Version 9.1.0) Dotmatics RRID:SCR_002798 R package limma (v. 3.58.1) Bioconductor RRID:SCR_010943 MaxQuant (v.1.5.2.8) MaxQuant RRID:SCR_014485 PhosphoSitePlus Kinase Library Johnson et al.61 https://kinase-library.phosphosite.org Snapgene (Version 5.0.8) GSL Biotech LLC RRID:SCR_015052 R package preprocessCore (Version 1.64.0) Bioconductor https://bioconductor.org/packages/ release/bioc/html/preprocessCore.html cutadapt (version see respective methods section) Martin89 https://cutadapt.readthedocs.io; RRID:SCR_011841 Bowtie2 (version 2.5.0) Langmead and Salzberg90 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml; RRID:SCR_016368 Samtools Li et al.91 http://samtools.sourceforge.net/; RRID:SCR_002105 STAR (version see respective methods section) Dobin et al.92 https://github.com/alexdobin/STAR; RRID:SCR_004463 Scikit-ribo, modified version Fang et al.93 Gao et al.94 https://github.com/nedialkova-lab/scikitribo-ext (Continued on next page) e4 Molecular Cell 86, 1275–1292.e1–e12, April 2, 2026 ..
Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Plasmid Preparation:Article Title: RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
Article Snippet: MS-5 mouse cells DSMZ ACC 441 .. Oligonucleotides Oligonucleotide sequences used in this study are provided in Table S9 This study N/A Recombinant DNA pcDNA5/FRT/TO-RNF25-WT-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRWD-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRING-mVenus3XFlag This study N/A pcDNA5/FRT/TO-mVenus-3xFlagGateway Di Fiore and Pines80 Addgene Plasmid #40999 pOG44_FLP_recombinase Hallacli et al.81 Addgene Plasmid #209087 Genome-wide All-in-One Brunello lentiviral library Doench et al.82 Addgene pooled library #73179 pX330-Puro Pritchard et al.83 Addgene Plasmid #82580 pU6-tevopreq1-GG-acceptor vector Nelson et al.84 Addgene Plasmid #174038 pU6-pegRNA-GG-acceptor vector Anzalone et al.85 Addgene Plasmid #132777 pCMV-PEmax Chen et al.86 Addgene Plasmid #174820 pEF1a-hMLH1dn Chen et al.86 Addgene Plasmid #174824 lentiGuide-Puro Sanjana et al.87 Addgene Plasmid #52963 pMDLg/pRRE Dull et al.88 Addgene Plasmid #12251 pRSV-Rev Dull et al.88 Addgene Plasmid #12253 pMD2.G/pVSV-g Didier Trono Addgene Plasmid #12259 Software and algorithms ImageLab (Version 5.2) Bio-Rad RRID:SCR_014210 SparkControl 3.1 Tecan https://lifesciences.tecan.com/multimode- plate-reader?p=tab–3 R (version 4.3.2) R Project for Statistical Computing RRID:SCR_001905 GraphPad Prism (Version 9.1.0) Dotmatics RRID:SCR_002798 R package limma (v. 3.58.1) Bioconductor RRID:SCR_010943 MaxQuant (v.1.5.2.8) MaxQuant RRID:SCR_014485 PhosphoSitePlus Kinase Library Johnson et al.61 https://kinase-library.phosphosite.org Snapgene (Version 5.0.8) GSL Biotech LLC RRID:SCR_015052 R package preprocessCore (Version 1.64.0) Bioconductor https://bioconductor.org/packages/ release/bioc/html/preprocessCore.html cutadapt (version see respective methods section) Martin89 https://cutadapt.readthedocs.io; RRID:SCR_011841 Bowtie2 (version 2.5.0) Langmead and Salzberg90 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml; RRID:SCR_016368 Samtools Li et al.91 http://samtools.sourceforge.net/; RRID:SCR_002105 STAR (version see respective methods section) Dobin et al.92 https://github.com/alexdobin/STAR; RRID:SCR_004463 Scikit-ribo, modified version Fang et al.93 Gao et al.94 https://github.com/nedialkova-lab/scikitribo-ext (Continued on next page) e4 Molecular Cell 86, 1275–1292.e1–e12, April 2, 2026 ..
Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Genome Wide:Article Title: RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
Article Snippet: MS-5 mouse cells DSMZ ACC 441 .. Oligonucleotides Oligonucleotide sequences used in this study are provided in Table S9 This study N/A Recombinant DNA pcDNA5/FRT/TO-RNF25-WT-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRWD-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRING-mVenus3XFlag This study N/A pcDNA5/FRT/TO-mVenus-3xFlagGateway Di Fiore and Pines80 Addgene Plasmid #40999 pOG44_FLP_recombinase Hallacli et al.81 Addgene Plasmid #209087 Genome-wide All-in-One Brunello lentiviral library Doench et al.82 Addgene pooled library #73179 pX330-Puro Pritchard et al.83 Addgene Plasmid #82580 pU6-tevopreq1-GG-acceptor vector Nelson et al.84 Addgene Plasmid #174038 pU6-pegRNA-GG-acceptor vector Anzalone et al.85 Addgene Plasmid #132777 pCMV-PEmax Chen et al.86 Addgene Plasmid #174820 pEF1a-hMLH1dn Chen et al.86 Addgene Plasmid #174824 lentiGuide-Puro Sanjana et al.87 Addgene Plasmid #52963 pMDLg/pRRE Dull et al.88 Addgene Plasmid #12251 pRSV-Rev Dull et al.88 Addgene Plasmid #12253 pMD2.G/pVSV-g Didier Trono Addgene Plasmid #12259 Software and algorithms ImageLab (Version 5.2) Bio-Rad RRID:SCR_014210 SparkControl 3.1 Tecan https://lifesciences.tecan.com/multimode- plate-reader?p=tab–3 R (version 4.3.2) R Project for Statistical Computing RRID:SCR_001905 GraphPad Prism (Version 9.1.0) Dotmatics RRID:SCR_002798 R package limma (v. 3.58.1) Bioconductor RRID:SCR_010943 MaxQuant (v.1.5.2.8) MaxQuant RRID:SCR_014485 PhosphoSitePlus Kinase Library Johnson et al.61 https://kinase-library.phosphosite.org Snapgene (Version 5.0.8) GSL Biotech LLC RRID:SCR_015052 R package preprocessCore (Version 1.64.0) Bioconductor https://bioconductor.org/packages/ release/bioc/html/preprocessCore.html cutadapt (version see respective methods section) Martin89 https://cutadapt.readthedocs.io; RRID:SCR_011841 Bowtie2 (version 2.5.0) Langmead and Salzberg90 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml; RRID:SCR_016368 Samtools Li et al.91 http://samtools.sourceforge.net/; RRID:SCR_002105 STAR (version see respective methods section) Dobin et al.92 https://github.com/alexdobin/STAR; RRID:SCR_004463 Scikit-ribo, modified version Fang et al.93 Gao et al.94 https://github.com/nedialkova-lab/scikitribo-ext (Continued on next page) e4 Molecular Cell 86, 1275–1292.e1–e12, April 2, 2026 ..
Software:Article Title: RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
Article Snippet: MS-5 mouse cells DSMZ ACC 441 .. Oligonucleotides Oligonucleotide sequences used in this study are provided in Table S9 This study N/A Recombinant DNA pcDNA5/FRT/TO-RNF25-WT-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRWD-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRING-mVenus3XFlag This study N/A pcDNA5/FRT/TO-mVenus-3xFlagGateway Di Fiore and Pines80 Addgene Plasmid #40999 pOG44_FLP_recombinase Hallacli et al.81 Addgene Plasmid #209087 Genome-wide All-in-One Brunello lentiviral library Doench et al.82 Addgene pooled library #73179 pX330-Puro Pritchard et al.83 Addgene Plasmid #82580 pU6-tevopreq1-GG-acceptor vector Nelson et al.84 Addgene Plasmid #174038 pU6-pegRNA-GG-acceptor vector Anzalone et al.85 Addgene Plasmid #132777 pCMV-PEmax Chen et al.86 Addgene Plasmid #174820 pEF1a-hMLH1dn Chen et al.86 Addgene Plasmid #174824 lentiGuide-Puro Sanjana et al.87 Addgene Plasmid #52963 pMDLg/pRRE Dull et al.88 Addgene Plasmid #12251 pRSV-Rev Dull et al.88 Addgene Plasmid #12253 pMD2.G/pVSV-g Didier Trono Addgene Plasmid #12259 Software and algorithms ImageLab (Version 5.2) Bio-Rad RRID:SCR_014210 SparkControl 3.1 Tecan https://lifesciences.tecan.com/multimode- plate-reader?p=tab–3 R (version 4.3.2) R Project for Statistical Computing RRID:SCR_001905 GraphPad Prism (Version 9.1.0) Dotmatics RRID:SCR_002798 R package limma (v. 3.58.1) Bioconductor RRID:SCR_010943 MaxQuant (v.1.5.2.8) MaxQuant RRID:SCR_014485 PhosphoSitePlus Kinase Library Johnson et al.61 https://kinase-library.phosphosite.org Snapgene (Version 5.0.8) GSL Biotech LLC RRID:SCR_015052 R package preprocessCore (Version 1.64.0) Bioconductor https://bioconductor.org/packages/ release/bioc/html/preprocessCore.html cutadapt (version see respective methods section) Martin89 https://cutadapt.readthedocs.io; RRID:SCR_011841 Bowtie2 (version 2.5.0) Langmead and Salzberg90 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml; RRID:SCR_016368 Samtools Li et al.91 http://samtools.sourceforge.net/; RRID:SCR_002105 STAR (version see respective methods section) Dobin et al.92 https://github.com/alexdobin/STAR; RRID:SCR_004463 Scikit-ribo, modified version Fang et al.93 Gao et al.94 https://github.com/nedialkova-lab/scikitribo-ext (Continued on next page) e4 Molecular Cell 86, 1275–1292.e1–e12, April 2, 2026 ..
Modification:Article Title: RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
Article Snippet: MS-5 mouse cells DSMZ ACC 441 .. Oligonucleotides Oligonucleotide sequences used in this study are provided in Table S9 This study N/A Recombinant DNA pcDNA5/FRT/TO-RNF25-WT-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRWD-mVenus3XFlag This study N/A pcDNA5/FRT/TO-RNF25-ΔRING-mVenus3XFlag This study N/A pcDNA5/FRT/TO-mVenus-3xFlagGateway Di Fiore and Pines80 Addgene Plasmid #40999 pOG44_FLP_recombinase Hallacli et al.81 Addgene Plasmid #209087 Genome-wide All-in-One Brunello lentiviral library Doench et al.82 Addgene pooled library #73179 pX330-Puro Pritchard et al.83 Addgene Plasmid #82580 pU6-tevopreq1-GG-acceptor vector Nelson et al.84 Addgene Plasmid #174038 pU6-pegRNA-GG-acceptor vector Anzalone et al.85 Addgene Plasmid #132777 pCMV-PEmax Chen et al.86 Addgene Plasmid #174820 pEF1a-hMLH1dn Chen et al.86 Addgene Plasmid #174824 lentiGuide-Puro Sanjana et al.87 Addgene Plasmid #52963 pMDLg/pRRE Dull et al.88 Addgene Plasmid #12251 pRSV-Rev Dull et al.88 Addgene Plasmid #12253 pMD2.G/pVSV-g Didier Trono Addgene Plasmid #12259 Software and algorithms ImageLab (Version 5.2) Bio-Rad RRID:SCR_014210 SparkControl 3.1 Tecan https://lifesciences.tecan.com/multimode- plate-reader?p=tab–3 R (version 4.3.2) R Project for Statistical Computing RRID:SCR_001905 GraphPad Prism (Version 9.1.0) Dotmatics RRID:SCR_002798 R package limma (v. 3.58.1) Bioconductor RRID:SCR_010943 MaxQuant (v.1.5.2.8) MaxQuant RRID:SCR_014485 PhosphoSitePlus Kinase Library Johnson et al.61 https://kinase-library.phosphosite.org Snapgene (Version 5.0.8) GSL Biotech LLC RRID:SCR_015052 R package preprocessCore (Version 1.64.0) Bioconductor https://bioconductor.org/packages/ release/bioc/html/preprocessCore.html cutadapt (version see respective methods section) Martin89 https://cutadapt.readthedocs.io; RRID:SCR_011841 Bowtie2 (version 2.5.0) Langmead and Salzberg90 http://bowtie-bio.sourceforge.net/bowtie2/ index.shtml; RRID:SCR_016368 Samtools Li et al.91 http://samtools.sourceforge.net/; RRID:SCR_002105 STAR (version see respective methods section) Dobin et al.92 https://github.com/alexdobin/STAR; RRID:SCR_004463 Scikit-ribo, modified version Fang et al.93 Gao et al.94 https://github.com/nedialkova-lab/scikitribo-ext (Continued on next page) e4 Molecular Cell 86, 1275–1292.e1–e12, April 2, 2026 ..
Produced:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Purification:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Virus:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Article Title: Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Electrocompetent E. coli bacteria New England Biolabs Cat#C3020K Lentiviral Larry Barcode Library Derived from AddGene Pooled Library #140024 Antibodies anti-CD235a BUV395 (Clone GA-R2) BD Biosciences RRID:AB_2739426 anti-CD41 AF700 (clone HIP8) Biolegend RRID:AB_2566538 anti-CD11b antibody Biolegend RRID: AB_314162 Reagents Thermolabile Exonuclease I New England Biolabs Cat#M0568L Agencourt AMPure beads Beckman Coulter Cat#A63881 AflII New England Biolabs Cat#R0520S AgeI-HF New England Biolabs Cat#R3552S T4 DNA ligase New England Biolabs Cat#M0202L NaeI New England Biolabs Cat#R0190S DpnI New England Biolabs Cat#R0176L BamHI-HF New England Biolabs Cat#R3136L KpnI-HF New England Biolabs Cat#R3142L Shrimp Phosphatase New England Biolabs Cat#M0371S DNase I (RNase-free) New England Biolabs Cat#M0303L on-column DNase I Quiagen Cat#79254 Turbo Dnase Invitrogen Cat#AM1907 SuperScript IV ThermoFisher Cat#18090050 RNasin Promega Cat#N261A Alt-R TM S.p. .. Cas9 Nuclease V3 IDT Cat#1081059 Trichostatin A (TSA) Selleckem Cat#S1045 M3814 Selleckem Cat#S8586 5nM phorbol 12-myristate 13-acetate (PMA) Selleckchem Cat#S7791 Chroman-1 MedChemExpress Cat#HY-15392 Emricasan Merck Cat#SML2227 trans-ISRIB R&D Cat#5284/10 Polyamine Supplement Merck Cat#P8483 BG iMatrix-511 Silk Tebubio Cat#348RL511S ART558 Selleckchem Cat#S9936 AZD468 MedChemExpress Cat#HY-111783 DAPI Sigma Aldrich Cat#D9542 Propidium Iodide Solution Sigma Aldrich Cat#537060 Critical commercial assays StemDiff Monocyte kit Stem Cell Technologies 05320 Kapa HiFi HS Ready Mix Kapa Biosystems Cat#07983034001 KAPA2G GC Buffer Roche Cat#KK5516 pGEM T easy system Promega Cat#A1360 Gibson Assembly® Cloning Kit New England Biolabs Cat#E5510S KAPA Illumina SYBR Universal Lib Q.
CRISPR:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Article Title: A Molecular Switch between Mammalian MLL Complexes Dictates Response to Menin–MLL Inhibition
Article Snippet: .. Paired mouse genome-scale CRISPR–Cas9 screening libraries (M1/M2) were used (Addgene Pooled Library #1000000173). ..
Gene Knockout:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Infection:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
Transfection:Article Title: The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-Histone H2A.X (Ser139) (D7T2V) Mouse mAb Cell Signaling Technology Cat# 80312; RRID: AB_2799949 p53 (DO-7) Mouse mAb Cell Signaling Technology Cat# 48818; RRID: AB_2713958 Phospho-p53 (Ser15) (16G8) Mouse mAb3 Cell Signaling Technology Cat# 9286; RRID: AB_331741 Monoclonal Anti-b-Actin antibody produced n mouse Sigma Aldrich Cat# A5441; RRID: AB_476744 Purified Mouse Anti-OPA1 monoclonal BD Biosciences CAT# 612607; RRID: AB_399889 Mouse monoclonal anti-OMA1 Santa Cruz Cat# sc-515788; RRID: AB_2905488 ATF-4 (D4B8) Rabbit mAb Cell Signaling Technology Cat# 11815: RRID: AB_2616025 PARP1 Polyclonal Antibody from Rabbit Thermo Fisher Cat# PA3-951; RRID: AB_2160723 Cleaved Caspase-3 (Asp175) Antibody Cell Signaling Technology Cat# 9661; RRID: AB_2341188 Anti-SDHA antibody mouse monoclonal Abcam Cat# ab14715; RRID: AB_301433 HRP-conjugated secondary antibody, anti-rabbit BioRad Cat# 170-6515: RRID: AB_11125142 HRP-conjugated secondary antibody, anti-mouse BioRad Cat# 170-6516: RRID: AB_11125547 Bacterial and virus strains Plasmid pLenti-Cas9-GFP Wang et al.84 Addgene Plasmid #86145 Packaging plasmid pCMV-dR8.2 dvpr Stewart et al.85 Addgene Plasmid #8455 Envelope plasmid pCMV-VSV-G Stewart et al.85 Addgene Plasmid #8454 Human CRISPR Metabolic Gene Knockout Library Laboratory of Lena Pernas, from Birsoy et al.35 Addgene Pooled Library #110066 Chemicals, peptides, and recombinant proteins Polybrene Infection/Transfection Reagent Sigma Aldrich TR-1003-G X-tremeGENETM 9 DNA transfection reagent Sigma Aldrich 6365779001 Lenti-X Concentrator Takara Bio USA, Inc. 631232 NEBNext Ultra II Q5 Master Mix New Englad BioLabs , Inc. M0544S YOYO-1 Iodide (491/509) Invitrogen Y3601 5-fluorouracil (5-FU) Sigma Aldrich F6627 Actinomycin D Sigma Aldrich A9415 Hydroxyurea (HU) Sigma Aldrich H8627 Etoposide Sigma Aldrich E1383 Doxorubicin hydrocloride Sigma Aldrich D1515 Carbonyl cyanide 3-chlorophenylhydrazone (CCCP) Sigma Aldrich C2759 Pifithrin-a (PFT-a) Sigma Aldrich P4359 Nutlin-3a Sigma Aldrich SML0580 Z-VAD-FMK Sigma Aldrich 219007 Uridine Sigma Aldrich U3003 Thymidine Sigma Aldrich T1895 Rotenone Sigma Aldrich R8875 Dimethyl malonate (DMM) Sigma Aldrich 135441 Antimycin A from Streptomyces sp. Sigma Aldrich A8674 Sodium azide Sigma Aldrich S8032 Oligomycin from Streptomyces diastatochromogenes Sigma Aldrich O4976 (Continued on next page) 18 Cell Reports 42, 112332, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER 2-deoxyglucose (2-DG) Sigma Aldrich D8375 TEPP-46 Sigma Aldrich 505487 D-Glucose-13C6 Sigma Aldrich 389374 GoScriptTM Reverse Transcription Mix Promega A2791 PowerSYBR Green PCR Master Mix Thermo Fisher Scientific 4368708 Critical commercial assays Lenti-X Packaging Single Shots Takara Bio USA, Inc. 631276 QIAamp DNA Blood Midi/Maxi Kit QIAGEN 51183 Deposited data Whole cell proteome from MEFs This paper ProteomeXchange: PXD036595 Metabolomics data from MEFs This paper Zenodo: https://doi.org/10.5281/ zenodo.7732867 Experimental models: Cell lines Homo sapiens 293T cells ATCC CRL-3216 Homo sapiens K562 cells, WT and OMA1 / This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Oma1 / Anand et al.13 N/A Homo sapiens HEK 293 cells, WT and OMA1 / Baker et al.6 N/A Mus musculus C2C12 myoblasts, WT and Oma1 / This paper N/A Homo sapiens HeLa cells This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Bax / Bak / Laboratory of Richard Youle (NINDS) N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Opa1V1D4/V1D4 This paper N/A Immortalized Mus musculus embryonic fibroblasts (MEFs), WT and Dele1 / This paper N/A Experimental models: Organisms/Strains Mouse: Opa1v1D4/V1D4 This paper N/A Mouse: Dele1 / Ahola et al.25 N/A Oligonucleotides See Table S3 N/A N/A Recombinant DNA pLVX-Puro-mOma1(WT)-Flag This paper N/A pLVX-Puro-mOma1(E324Q)-Flag This paper N/A Software and algorithms IncuCyte S3 Software Sartorius v2021C ImageJ 1.52a Public domain https://ImageJ.nih.gov/ij/ Prism 9 Graph Pad https://www.graphpad.com Quant Studio v.1.4.3.
other:Article Title: Phenotypic screens for SIRPA expression reveal RAB21 as a general regulator of macrophage surface identity.
Article Snippet: 7.0.1.4 Thermo Scientific Cat#5187139 CFX ManagerTM Software Bio-Rad Cat#1845000 Fiji http://fiji.sc RRID:SCR_002285 Bio-Formats https://www.openmicroscopy.org/ site/products/bio-formats RRID:SCR_000450 NEBuilder assembly tool https://nebuilder.neb.com/ NA AlphaFold Server https://alphafoldserver.com/ NA PAE Viewer https://subtiwiki.uni-goettingen.de/ v4/paeViewerDemo NA UCSF ChimeraX https://www.cgl.ucsf.edu/chimerax/ RRID:SCR_015872 Conserved Domain Database https://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml RRID:SCR_002077 Other C1000 TouchTM Thermal Cycler with 96-Well Fast Reaction Module Bio-Rad Cat#1851196 OwlTM EasyCastTM B1 Mini Gel Electrophoresis Systems Thermo Scientific Cat#B1-BP PowerPacTM HC Power Supply Bio-Rad Cat#1645052 BluPAD Dual LED Blue/White Light Transilluminator Bio-Helix Cat#BP001CU NanoDropTM One/OneC Microvolume UV-Vis Spectrophotometer Thermo Scientific Cat#ND-ONE-W iBrightTM FL1500 system Invitrogen Cat#A44241 Mini gel tank Invitrogen Cat#A25977 Immobilon®-P PVDF Membrane Millipore Cat#IPVH00010 Mini blot module Invitrogen Cat#B1000 iBlotTM 3 Western Blot Transfer Device Invitrogen Cat#IB31001 iBlotTM 3 Transfer Stacks, midi, PVDF Invitrogen Cat#IB34001 S3eTM Cell Sorter Bio-Rad Cat#1451006 LSR II Flow Cytometer BD Biosciences discontinued FACSymphonyTM A3 Cell Analyzer BD Biosciences Through quote CytoFLEX LX Flow Cytometer Beckman Coulter Through quote IntelliCyt® iQue Screener PLUS Sartorius Through quote Falcon® 5 mL Round Bottom Polystyrene Test Tube, with Cell Strainer Snap Cap Corning Cat#352235 VWR® Cell Strainers, DNase/RNase Free, Non-Pyrogenic, Sterile VWR Cat#76327-100 (Continued on next page) 24 Cell Reports 44, 115921, July 22, 2025
Bacteria:Article Title: Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Electrocompetent E. coli bacteria New England Biolabs Cat#C3020K Lentiviral Larry Barcode Library Derived from AddGene Pooled Library #140024 Antibodies anti-CD235a BUV395 (Clone GA-R2) BD Biosciences RRID:AB_2739426 anti-CD41 AF700 (clone HIP8) Biolegend RRID:AB_2566538 anti-CD11b antibody Biolegend RRID: AB_314162 Reagents Thermolabile Exonuclease I New England Biolabs Cat#M0568L Agencourt AMPure beads Beckman Coulter Cat#A63881 AflII New England Biolabs Cat#R0520S AgeI-HF New England Biolabs Cat#R3552S T4 DNA ligase New England Biolabs Cat#M0202L NaeI New England Biolabs Cat#R0190S DpnI New England Biolabs Cat#R0176L BamHI-HF New England Biolabs Cat#R3136L KpnI-HF New England Biolabs Cat#R3142L Shrimp Phosphatase New England Biolabs Cat#M0371S DNase I (RNase-free) New England Biolabs Cat#M0303L on-column DNase I Quiagen Cat#79254 Turbo Dnase Invitrogen Cat#AM1907 SuperScript IV ThermoFisher Cat#18090050 RNasin Promega Cat#N261A Alt-R TM S.p. .. Cas9 Nuclease V3 IDT Cat#1081059 Trichostatin A (TSA) Selleckem Cat#S1045 M3814 Selleckem Cat#S8586 5nM phorbol 12-myristate 13-acetate (PMA) Selleckchem Cat#S7791 Chroman-1 MedChemExpress Cat#HY-15392 Emricasan Merck Cat#SML2227 trans-ISRIB R&D Cat#5284/10 Polyamine Supplement Merck Cat#P8483 BG iMatrix-511 Silk Tebubio Cat#348RL511S ART558 Selleckchem Cat#S9936 AZD468 MedChemExpress Cat#HY-111783 DAPI Sigma Aldrich Cat#D9542 Propidium Iodide Solution Sigma Aldrich Cat#537060 Critical commercial assays StemDiff Monocyte kit Stem Cell Technologies 05320 Kapa HiFi HS Ready Mix Kapa Biosystems Cat#07983034001 KAPA2G GC Buffer Roche Cat#KK5516 pGEM T easy system Promega Cat#A1360 Gibson Assembly® Cloning Kit New England Biolabs Cat#E5510S KAPA Illumina SYBR Universal Lib Q.
Derivative Assay:Article Title: Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Electrocompetent E. coli bacteria New England Biolabs Cat#C3020K Lentiviral Larry Barcode Library Derived from AddGene Pooled Library #140024 Antibodies anti-CD235a BUV395 (Clone GA-R2) BD Biosciences RRID:AB_2739426 anti-CD41 AF700 (clone HIP8) Biolegend RRID:AB_2566538 anti-CD11b antibody Biolegend RRID: AB_314162 Reagents Thermolabile Exonuclease I New England Biolabs Cat#M0568L Agencourt AMPure beads Beckman Coulter Cat#A63881 AflII New England Biolabs Cat#R0520S AgeI-HF New England Biolabs Cat#R3552S T4 DNA ligase New England Biolabs Cat#M0202L NaeI New England Biolabs Cat#R0190S DpnI New England Biolabs Cat#R0176L BamHI-HF New England Biolabs Cat#R3136L KpnI-HF New England Biolabs Cat#R3142L Shrimp Phosphatase New England Biolabs Cat#M0371S DNase I (RNase-free) New England Biolabs Cat#M0303L on-column DNase I Quiagen Cat#79254 Turbo Dnase Invitrogen Cat#AM1907 SuperScript IV ThermoFisher Cat#18090050 RNasin Promega Cat#N261A Alt-R TM S.p. .. Cas9 Nuclease V3 IDT Cat#1081059 Trichostatin A (TSA) Selleckem Cat#S1045 M3814 Selleckem Cat#S8586 5nM phorbol 12-myristate 13-acetate (PMA) Selleckchem Cat#S7791 Chroman-1 MedChemExpress Cat#HY-15392 Emricasan Merck Cat#SML2227 trans-ISRIB R&D Cat#5284/10 Polyamine Supplement Merck Cat#P8483 BG iMatrix-511 Silk Tebubio Cat#348RL511S ART558 Selleckchem Cat#S9936 AZD468 MedChemExpress Cat#HY-111783 DAPI Sigma Aldrich Cat#D9542 Propidium Iodide Solution Sigma Aldrich Cat#537060 Critical commercial assays StemDiff Monocyte kit Stem Cell Technologies 05320 Kapa HiFi HS Ready Mix Kapa Biosystems Cat#07983034001 KAPA2G GC Buffer Roche Cat#KK5516 pGEM T easy system Promega Cat#A1360 Gibson Assembly® Cloning Kit New England Biolabs Cat#E5510S KAPA Illumina SYBR Universal Lib Q.
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