Lactate Assay:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Picogreen Assay:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Library Quantification:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Bicinchoninic Acid Protein Assay:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Purification:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
RNA Sequencing:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Recombinant:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
shRNA:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Plasmid Preparation:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Control:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Software:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Ubiquitin linkage-specific K48 antibody Abcam Cat#ab140601; RRID:AB_2783797 Anti-pan Kla antibody PTM Biolabs Cat#PTM-1401; RRID:AB_2868521 Ultra-LEAF Purified anti-human CD64 (FcgR), Clone 10.1 Biolegend Cat#305047; RRID:AB_2810455 Biological samples Human Bone Marrow CD34+ Cells, Frozen StemCell Technologies, Inc. Cat#70002.3 Chemicals, peptides, and recombinant proteins Human Recombinant SCF StemCell Technologies, Inc. Cat#78062 PROCRIT Janssen N/A Dexamethasone Sigma–Aldrich Cat#D2915-100MG Human Recombinant IGF-I StemCell Technologies, Inc. Cat#78022 Human Recombinant IL-3, ACF StemCell Technologies, Inc. Cat#78146.1 Human recombinant insulin Santa Cruz Biotech Cat#sc-360248 3,30,5-Triiodo-L-thyronine sodium salt Sigma–Aldrich Cat#T6397-100MG Holo-Transferrin Santa Cruz Biotech Cat#sc-391098A UK 5099 Santa Cruz Biotech Cat#sc-361394 Dimethyloxaloylglycine (DMOG) Santa Cruz Biotech Cat#sc-200755 Sodium oxamate Santa Cruz Biotech Cat#sc-215880 Digoxin Sigma–Aldrich Cat#D6003-100MG MG-132 Santa Cruz Biotech Cat#sc-201270 Bortezomib Santa Cruz Biotech Cat#sc-217785 Bafilomycin A1 Ready-Made Solution Sigma–Aldrich Cat#SML1661-.1ML Pepstatin A Sigma–Aldrich Cat#P5318-5MG E-64d Sigma–Aldrich Cat#E8640-250UG 5,8,11,14-Eicosatetraynoic acid Sigma–Aldrich Cat#E1768-5MG Sodium L-lactate Sigma–Aldrich Cat#L7022-5G Intron A (interferon-alpha-2b recombinant) Schering-Plough N/A Puromycin dihydrochloride Santa Cruz Biotech Cat#sc-108071 LEUKINE (sargramostim) Partner Therapeutics N/A 20,30-Dideoxycytidine Sigma–Aldrich Cat#D5782-100MG pHrodo Red, succinimidyl ester (pHrodo Red, SE) Thermo Fisher Cat#P36600 Copper (II) sulfate Santa Cruz Biotech Cat#sc-211133 Sodium L-ascorbate Santa Cruz Biotech Cat#sc-215877 Calcium Chloride Santa Cruz Biotech Cat#sc-202091 A23187 Sigma–Aldrich Cat#C7522-1MG Poly dA:dT/ LyoVec Invivogen Cat#tlrl-patc Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone Santa Cruz Biotech Cat#sc-203578 Glutaraldehyde solution Sigma–Aldrich Cat#G5882-10X1ML Picric acid solution Sigma–Aldrich Cat#P6744-1GA Osmium tetroxide Sigma–Aldrich Cat# 201030-100MG Potassium ferricyanide (III) Sigma–Aldrich Cat#702587-50G Oligomycin A Santa Cruz Biotech Cat#sc-201551 Antimycin A Santa Cruz Biotech Cat#sc-202467 Rotenone Santa Cruz Biotech Cat#sc-203242 BPTES Sigma–Aldrich Cat#SML0601-5MG Etomoxir Santa Cruz Biotech Cat#sc-215009 D(+)Glucose Santa Cruz Biotech Cat#sc-211203 Suc-Leu-Leu-Val-Tyr-AMC Enzo Cat#BML-P802-0005 (Continued on next page) ll Cell 184, 4464–4479.e1–e9, August 19, 2021 e2 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER BZ-Val-Gly-Arg-AMC Enzo Cat#BML-BW9375-0005 Z-Leu-Leu-Glu-AMC Enzo Cat#BML-ZW9345-0005 Human 26S Proteasome Protein R&D Systems Cat#E-365-050 Sodium acetate Sigma–Aldrich Cat#S2889 Sodium succinate Sigma–Aldrich Cat#14160 Sodium malonate Sigma–Aldrich Cat#63409 Sodium L-lactate Sigma–Aldrich Cat#L7022 L-lactic acid Santa Cruz Biotech Cat#sc-391063 Epoxomicin Sigma–Aldrich Cat#E3652-50UG 2-iodoacetamide Sigma–Aldrich Cat#I1149 Endoproteinase LysC New England Biolabs Cat#P8109S Trypsin Sigma–Aldrich Cat#T4799-5G L-Aspartic acid Sigma–Aldrich Cat#A7219 Critical commercial assays Lineage Cell Depletion Kit, human Miltenyi Biotec Cat#130-092-211 Human CD34+ Cell NucleofectorTM Kit Lonza Cat#VPA-1003 EasySep Human Monocyte Enrichment Kit StemCell Technologies, Inc. Cat#19059 CellTrace CFSE Cell Proliferation Kit Thermo Fisher Cat#C34554 Human IFN-a Flex Set BD Biosciences Cat#560379 Human TNF Flex Set BD Biosciences Cat#558273 CD71 MicroBeads, human Miltenyi Biotec Cat#130-046-201 CD15 MicroBeads, human Miltenyi Biotec Cat#130-046-601 Lactate Assay Kit Sigma–Aldrich Cat#MAK064-1KT Quant-iT PicoGreen dsDNA Assay Kit Thermo Fisher Cat#P7589 RNeasy Micro Kit QIAGEN Cat#74004 KAPA RNA HyperPrep Kit KAPA Biosystems Cat#KK8540 KAPA Library Quantification Kit KAPA Biosystems Cat#KK4824 BCA Protein Assay Kit Thermo Fisher Cat#23225 Proteasome purification kit Enzo Cat#BML-PW1075A-0001 Deposited data Raw and analyzed RNA-seq data This paper GEO: GSE163073 Oligonucleotides cGAS ON-TARGETplus siRNA Reagents Horizon Cat#L-015607-02-0005 STING1 ON-TARGETplus siRNA Reagents Horizon Cat#L-024333-00-0005 IRF3 ON-TARGETplus siRNA Reagents Horizon Cat#L-006875-00-0005 ND1 Forward; 50-GCATTCCTAATGCTTACCGAAC-30 Caielli et al., 2016 N/A ND1 Reverse; 50-AAGGGTGGAGAGGTTAAAGGAG-30 Caielli et al., 2016 N/A GAPDH Forward; 50-AGGCAACTAGGATGGTGTGG-30 Caielli et al., 2016 N/A GAPHD Reverse; 50-TTGATTTTGGAGGGATCTCG-30 Caielli et al., 2016 N/A Recombinant DNA 15-LO shRNA Plasmid (h) Santa Cruz Biotech Cat#sc-105003-SH Control shRNA Plasmid-A Santa Cruz Biotech Cat#sc-108060 copGFP Control shRNA Plasmid Santa Cruz Biotech Cat#sc-108083 Software and algorithms Flowjo v10 BD Biosciences RRID:SCR_008520 GraphPad Prism 9 GraphPad Software RRID:SCR_002798 Fiji/ImageJ https://imagej.net/software/fiji RRID:SCR_002285 (Continued on next page) ll e3 Cell 184, 4464–4479.e1–e9, August 19, 2021 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
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