Blocking Assay:Article Title: Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MCU Cell Signaling Cat#D2Z3B; RRID: AB_2721812 EMRE Santa Cruz Cat#86337; RRID: AB_2250685 MICU1 Atlas Antibodies Cat#HPA034780; RRID: AB_10696934 MICU2 Abcam Cat#ab101465 MICU3 Atlas Antibodies Cat# HPA024771; RRID: AB_1848022 VDAC Abcam Cat# ab14734 RRID: AB_443084 COX1 Abcam Cat#ab14705; RRID: AB_2084810 COX2 Abcam Cat#ab14734 Tim23 Santa Cruz Cat#sc-5114463 FLAG Sigma-Aldrich Cat#F1804; RRID: AB_262044 YME1L1 Proteintech Cat#11510-1-AP; RRID: AB_2217459 AFG3L2 Proteintech Cat#14631-1-AP; RRID: AB_2242420 Letm1 Abcam Cat#ab55434; RRID: AB_943985 b-actin Santa Cruz Cat#sc-69879; RRID: AB_1119529 NDUFS1 Santa Cruz Cat#sc-271510; RRID: AB10655669 NDUFS3 Santa Cruz Cat#sc-374282; RRID: AB_10991315 SDHA Santa Cruz Cat#sc-390381 Rieske Santa Cruz Cat#sc-271609 RRID: AB_10655682 ATP5F1 Santa Cruz Cat#sc-514419 1D4 Home made N/A PDH-E1ɑ Santa Cruz Cat#sc-377092 RRID: AB_2716767 S293 phosphorylated PDH-E1ɑ Millipore Cat#ABS204 RRID: AB_11205754 IRDye 680RD goat-anti rabbit LI-COR Cat#925-68071; RRID: AB_2721181 IRDye 800CW goat-anti mouse LI-COR Cat#925-32210; RRID: AB_2687825 IRDye 680RD goat-anti mouse LI-COR Cat#925-68070 RRID: AB_2651128 Alkaline phosphatase conjugated anti-rabbit secondary antibody Promega Cat# S373B Bacterial and virus strains E. coli: DH5ɑ competent cells New England Biolabs Cat#C2987H E. coli: BL21(DE3) Christopher Miller Tsai et al. (2012) Biological samples Left ventricular tissues of non-failing human hearts Adult Cardiac Tissue Bank at the University of Colorado DenverAnschutz Medical campus N/A Chemicals, peptides, and recombinant proteins Lipofectamine 3000 Life Technologies Cat#L3000150 Lipofectamine 2000 Life Technologies Cat#11668019 DDM, anagrade Anatrace Cat#D310 (Continued on next page) Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RIPA buffer Santa Cruz Cat#sc-24948 Intercept blocking buffer (TBS-based) LI-COR Cat#927-60001 PVDF membranes LI-COR Cat926-31097 Protease inhibitor cocktail tablet Roche Cat#05892970001 TALON cobalt affinity resin Takara Cat#635504 CNBr-activated Sepharose 4B GE Healthcare Cat#17043001 Cycloheximide Sigma Cat#C7698 Oligomycin Cayman Cat#11342 Rotenone Cayman Cat#13995 Antimycin A Sigma Cat#A8674 Ionomycin Cayman Cat#11932 Carbachol Cayman Cat#114486 45Ca2+ radioisotope Perkin-Elmer Cat#NEZ013001MC 35S-methionine Perkin-Elmer Cat#NEG009A001MC Cysteine/methionine free medium Sigma Cat#D0422 Protein A beads Santa Cruz Cat#sc-2001 Thapsigargin Cayman Cat#10522 Digitonin Sigma-Aldrich Cat#D141 Calcium green 5N Life Technologies Cat#C3737 TMRM Invitrogen Cat#T668 FCCP Cayman Cat#15218 Doxorubicin Tokyo Chemical Industry Cat#D4193 Cisplatin Tokyo Chemical Industry Cat#D3371 Annexin V CF488A Biotium Cat#29083 Propidium Iodide Cayman Cat#14289 Hoescht 33,258 Cayman Cat#16756 Luciferin ThermoFisher Cat#PI88291 Critical commercial assays Seahorse XF Real-time ATP Rate Assay Kit Agilent Cat#103591-100 QuickChange II Kit Agilent Cat#200524 BCA assay kit Thermo Cat#23225 NativePAGE Sample Prep kit Invitrogen Cat#BN2008 NativePAGE Running Buffer kit Invitrogen Cat#BN2007 Deposited data Unprocessed images used in the figures This paper https://doi.org/10.17632/shrtrdfhyt.1 Experimental models: Cell lines HEK 293T: wild type ATCC Cat#CRL-11268; RRID: CVCL_1926 HeLa: wild type ATCC Cat#CCL-2; RRID: CVCL_0030 U2OS: wild type Cell Technologies Resource Center in the University of Colorado Anschutz Medical Campus https://medschool.cuanschutz.edu/ colorado-cancer-center/research/ shared-resources/cell-technologies/ cell-culture-services HEK 293T: MICU1-KO Home made Tsai et al. (2017) HEK 293T: MICU2-KO Home made Fan et al. (2020) HEK 293T: MICU1-MICU2-KO Home made Fan et al. (2020) HEK 239T: C463R-MICU1 (CRISPR base edited) This paper N/A MEF cells: wild type Vivek Garg Garg et al. (2021) MEF cells: MICU1-KO Vivek Garg Garg et al. (2021) (Continued on next page) e2 Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER MEF cells: MICU2-KO Vivek Garg Garg et al. (2021) Experimental models: Organisms/strains C57BL/6J mouse: wild type Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000,664 Sprague-Dawley rats: wild type Charles River Laboratory Cat#001; RRID: RGD_734476 Oligonucleotides sgRNA sequence to mutate native MICU1 to C463R in HEK cells: 50-ACACCTTCCTGTGCACATTTCCACAG This paper N/A Recombinant DNA MCU, EMRE, MICU1 or MICU2 in pcDNA3.1(+) Home made Tsai et al. (2016); Tsai et al., 2017 MICU1 or MICU2 in pLJM1 This paper N/A pLKO.hygro constructs to knockdown YME1L1 or AFG3L2 Home made Tsai et al., 2017 pCMV_ABEmax Koblan et al. (2018) Addgene Cat#112095 MLM3636 sgRNA expression plasmid Keith Joung Addgene Cat#43860 Mito-GCaMP6f Timothy Ryan Ashrafi et al. (2020) Cyto-GCaMP6f Chen et al. (2013) Addgene Cat#40755 Mito-Sypher Poburko et al. (2011) Addgene Cat#48251 Cyto-Sypher Poburko et al. (2011) Addgene Cat#48250 Mito-roGFP2-Orp1 Gutscher et al. (2009) Addgene Cat#64992 Mitochondria-targeted luciferase Paolo Pinton Morciano et al. (2017) Mito-GEM-GECO1 Zhao et al. (2011) Addgene Cat#32461 MBP-MICU1 in pET24a This paper N/A MICU2 in pETDuet This paper N/A Software and algorithms Igor pro (version 8) WaveMetrics www.wavemetrics.com/products/igorpro Image Studio (version 5.2) LI-COR https://www.licor.com/bio/image-studio/ ImageJ (Mac OS X) ImageJ website https://ImageJ.nih.gov/ij Time Series Analyzer plug-in (version 3) Balaji J https://ImageJ.nih.gov/ij/plugins/time- series.html
Protease Inhibitor:Article Title: Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MCU Cell Signaling Cat#D2Z3B; RRID: AB_2721812 EMRE Santa Cruz Cat#86337; RRID: AB_2250685 MICU1 Atlas Antibodies Cat#HPA034780; RRID: AB_10696934 MICU2 Abcam Cat#ab101465 MICU3 Atlas Antibodies Cat# HPA024771; RRID: AB_1848022 VDAC Abcam Cat# ab14734 RRID: AB_443084 COX1 Abcam Cat#ab14705; RRID: AB_2084810 COX2 Abcam Cat#ab14734 Tim23 Santa Cruz Cat#sc-5114463 FLAG Sigma-Aldrich Cat#F1804; RRID: AB_262044 YME1L1 Proteintech Cat#11510-1-AP; RRID: AB_2217459 AFG3L2 Proteintech Cat#14631-1-AP; RRID: AB_2242420 Letm1 Abcam Cat#ab55434; RRID: AB_943985 b-actin Santa Cruz Cat#sc-69879; RRID: AB_1119529 NDUFS1 Santa Cruz Cat#sc-271510; RRID: AB10655669 NDUFS3 Santa Cruz Cat#sc-374282; RRID: AB_10991315 SDHA Santa Cruz Cat#sc-390381 Rieske Santa Cruz Cat#sc-271609 RRID: AB_10655682 ATP5F1 Santa Cruz Cat#sc-514419 1D4 Home made N/A PDH-E1ɑ Santa Cruz Cat#sc-377092 RRID: AB_2716767 S293 phosphorylated PDH-E1ɑ Millipore Cat#ABS204 RRID: AB_11205754 IRDye 680RD goat-anti rabbit LI-COR Cat#925-68071; RRID: AB_2721181 IRDye 800CW goat-anti mouse LI-COR Cat#925-32210; RRID: AB_2687825 IRDye 680RD goat-anti mouse LI-COR Cat#925-68070 RRID: AB_2651128 Alkaline phosphatase conjugated anti-rabbit secondary antibody Promega Cat# S373B Bacterial and virus strains E. coli: DH5ɑ competent cells New England Biolabs Cat#C2987H E. coli: BL21(DE3) Christopher Miller Tsai et al. (2012) Biological samples Left ventricular tissues of non-failing human hearts Adult Cardiac Tissue Bank at the University of Colorado DenverAnschutz Medical campus N/A Chemicals, peptides, and recombinant proteins Lipofectamine 3000 Life Technologies Cat#L3000150 Lipofectamine 2000 Life Technologies Cat#11668019 DDM, anagrade Anatrace Cat#D310 (Continued on next page) Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RIPA buffer Santa Cruz Cat#sc-24948 Intercept blocking buffer (TBS-based) LI-COR Cat#927-60001 PVDF membranes LI-COR Cat926-31097 Protease inhibitor cocktail tablet Roche Cat#05892970001 TALON cobalt affinity resin Takara Cat#635504 CNBr-activated Sepharose 4B GE Healthcare Cat#17043001 Cycloheximide Sigma Cat#C7698 Oligomycin Cayman Cat#11342 Rotenone Cayman Cat#13995 Antimycin A Sigma Cat#A8674 Ionomycin Cayman Cat#11932 Carbachol Cayman Cat#114486 45Ca2+ radioisotope Perkin-Elmer Cat#NEZ013001MC 35S-methionine Perkin-Elmer Cat#NEG009A001MC Cysteine/methionine free medium Sigma Cat#D0422 Protein A beads Santa Cruz Cat#sc-2001 Thapsigargin Cayman Cat#10522 Digitonin Sigma-Aldrich Cat#D141 Calcium green 5N Life Technologies Cat#C3737 TMRM Invitrogen Cat#T668 FCCP Cayman Cat#15218 Doxorubicin Tokyo Chemical Industry Cat#D4193 Cisplatin Tokyo Chemical Industry Cat#D3371 Annexin V CF488A Biotium Cat#29083 Propidium Iodide Cayman Cat#14289 Hoescht 33,258 Cayman Cat#16756 Luciferin ThermoFisher Cat#PI88291 Critical commercial assays Seahorse XF Real-time ATP Rate Assay Kit Agilent Cat#103591-100 QuickChange II Kit Agilent Cat#200524 BCA assay kit Thermo Cat#23225 NativePAGE Sample Prep kit Invitrogen Cat#BN2008 NativePAGE Running Buffer kit Invitrogen Cat#BN2007 Deposited data Unprocessed images used in the figures This paper https://doi.org/10.17632/shrtrdfhyt.1 Experimental models: Cell lines HEK 293T: wild type ATCC Cat#CRL-11268; RRID: CVCL_1926 HeLa: wild type ATCC Cat#CCL-2; RRID: CVCL_0030 U2OS: wild type Cell Technologies Resource Center in the University of Colorado Anschutz Medical Campus https://medschool.cuanschutz.edu/ colorado-cancer-center/research/ shared-resources/cell-technologies/ cell-culture-services HEK 293T: MICU1-KO Home made Tsai et al. (2017) HEK 293T: MICU2-KO Home made Fan et al. (2020) HEK 293T: MICU1-MICU2-KO Home made Fan et al. (2020) HEK 239T: C463R-MICU1 (CRISPR base edited) This paper N/A MEF cells: wild type Vivek Garg Garg et al. (2021) MEF cells: MICU1-KO Vivek Garg Garg et al. (2021) (Continued on next page) e2 Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER MEF cells: MICU2-KO Vivek Garg Garg et al. (2021) Experimental models: Organisms/strains C57BL/6J mouse: wild type Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000,664 Sprague-Dawley rats: wild type Charles River Laboratory Cat#001; RRID: RGD_734476 Oligonucleotides sgRNA sequence to mutate native MICU1 to C463R in HEK cells: 50-ACACCTTCCTGTGCACATTTCCACAG This paper N/A Recombinant DNA MCU, EMRE, MICU1 or MICU2 in pcDNA3.1(+) Home made Tsai et al. (2016); Tsai et al., 2017 MICU1 or MICU2 in pLJM1 This paper N/A pLKO.hygro constructs to knockdown YME1L1 or AFG3L2 Home made Tsai et al., 2017 pCMV_ABEmax Koblan et al. (2018) Addgene Cat#112095 MLM3636 sgRNA expression plasmid Keith Joung Addgene Cat#43860 Mito-GCaMP6f Timothy Ryan Ashrafi et al. (2020) Cyto-GCaMP6f Chen et al. (2013) Addgene Cat#40755 Mito-Sypher Poburko et al. (2011) Addgene Cat#48251 Cyto-Sypher Poburko et al. (2011) Addgene Cat#48250 Mito-roGFP2-Orp1 Gutscher et al. (2009) Addgene Cat#64992 Mitochondria-targeted luciferase Paolo Pinton Morciano et al. (2017) Mito-GEM-GECO1 Zhao et al. (2011) Addgene Cat#32461 MBP-MICU1 in pET24a This paper N/A MICU2 in pETDuet This paper N/A Software and algorithms Igor pro (version 8) WaveMetrics www.wavemetrics.com/products/igorpro Image Studio (version 5.2) LI-COR https://www.licor.com/bio/image-studio/ ImageJ (Mac OS X) ImageJ website https://ImageJ.nih.gov/ij Time Series Analyzer plug-in (version 3) Balaji J https://ImageJ.nih.gov/ij/plugins/time- series.html
BIA-KA:Article Title: Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MCU Cell Signaling Cat#D2Z3B; RRID: AB_2721812 EMRE Santa Cruz Cat#86337; RRID: AB_2250685 MICU1 Atlas Antibodies Cat#HPA034780; RRID: AB_10696934 MICU2 Abcam Cat#ab101465 MICU3 Atlas Antibodies Cat# HPA024771; RRID: AB_1848022 VDAC Abcam Cat# ab14734 RRID: AB_443084 COX1 Abcam Cat#ab14705; RRID: AB_2084810 COX2 Abcam Cat#ab14734 Tim23 Santa Cruz Cat#sc-5114463 FLAG Sigma-Aldrich Cat#F1804; RRID: AB_262044 YME1L1 Proteintech Cat#11510-1-AP; RRID: AB_2217459 AFG3L2 Proteintech Cat#14631-1-AP; RRID: AB_2242420 Letm1 Abcam Cat#ab55434; RRID: AB_943985 b-actin Santa Cruz Cat#sc-69879; RRID: AB_1119529 NDUFS1 Santa Cruz Cat#sc-271510; RRID: AB10655669 NDUFS3 Santa Cruz Cat#sc-374282; RRID: AB_10991315 SDHA Santa Cruz Cat#sc-390381 Rieske Santa Cruz Cat#sc-271609 RRID: AB_10655682 ATP5F1 Santa Cruz Cat#sc-514419 1D4 Home made N/A PDH-E1ɑ Santa Cruz Cat#sc-377092 RRID: AB_2716767 S293 phosphorylated PDH-E1ɑ Millipore Cat#ABS204 RRID: AB_11205754 IRDye 680RD goat-anti rabbit LI-COR Cat#925-68071; RRID: AB_2721181 IRDye 800CW goat-anti mouse LI-COR Cat#925-32210; RRID: AB_2687825 IRDye 680RD goat-anti mouse LI-COR Cat#925-68070 RRID: AB_2651128 Alkaline phosphatase conjugated anti-rabbit secondary antibody Promega Cat# S373B Bacterial and virus strains E. coli: DH5ɑ competent cells New England Biolabs Cat#C2987H E. coli: BL21(DE3) Christopher Miller Tsai et al. (2012) Biological samples Left ventricular tissues of non-failing human hearts Adult Cardiac Tissue Bank at the University of Colorado DenverAnschutz Medical campus N/A Chemicals, peptides, and recombinant proteins Lipofectamine 3000 Life Technologies Cat#L3000150 Lipofectamine 2000 Life Technologies Cat#11668019 DDM, anagrade Anatrace Cat#D310 (Continued on next page) Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RIPA buffer Santa Cruz Cat#sc-24948 Intercept blocking buffer (TBS-based) LI-COR Cat#927-60001 PVDF membranes LI-COR Cat926-31097 Protease inhibitor cocktail tablet Roche Cat#05892970001 TALON cobalt affinity resin Takara Cat#635504 CNBr-activated Sepharose 4B GE Healthcare Cat#17043001 Cycloheximide Sigma Cat#C7698 Oligomycin Cayman Cat#11342 Rotenone Cayman Cat#13995 Antimycin A Sigma Cat#A8674 Ionomycin Cayman Cat#11932 Carbachol Cayman Cat#114486 45Ca2+ radioisotope Perkin-Elmer Cat#NEZ013001MC 35S-methionine Perkin-Elmer Cat#NEG009A001MC Cysteine/methionine free medium Sigma Cat#D0422 Protein A beads Santa Cruz Cat#sc-2001 Thapsigargin Cayman Cat#10522 Digitonin Sigma-Aldrich Cat#D141 Calcium green 5N Life Technologies Cat#C3737 TMRM Invitrogen Cat#T668 FCCP Cayman Cat#15218 Doxorubicin Tokyo Chemical Industry Cat#D4193 Cisplatin Tokyo Chemical Industry Cat#D3371 Annexin V CF488A Biotium Cat#29083 Propidium Iodide Cayman Cat#14289 Hoescht 33,258 Cayman Cat#16756 Luciferin ThermoFisher Cat#PI88291 Critical commercial assays Seahorse XF Real-time ATP Rate Assay Kit Agilent Cat#103591-100 QuickChange II Kit Agilent Cat#200524 BCA assay kit Thermo Cat#23225 NativePAGE Sample Prep kit Invitrogen Cat#BN2008 NativePAGE Running Buffer kit Invitrogen Cat#BN2007 Deposited data Unprocessed images used in the figures This paper https://doi.org/10.17632/shrtrdfhyt.1 Experimental models: Cell lines HEK 293T: wild type ATCC Cat#CRL-11268; RRID: CVCL_1926 HeLa: wild type ATCC Cat#CCL-2; RRID: CVCL_0030 U2OS: wild type Cell Technologies Resource Center in the University of Colorado Anschutz Medical Campus https://medschool.cuanschutz.edu/ colorado-cancer-center/research/ shared-resources/cell-technologies/ cell-culture-services HEK 293T: MICU1-KO Home made Tsai et al. (2017) HEK 293T: MICU2-KO Home made Fan et al. (2020) HEK 293T: MICU1-MICU2-KO Home made Fan et al. (2020) HEK 239T: C463R-MICU1 (CRISPR base edited) This paper N/A MEF cells: wild type Vivek Garg Garg et al. (2021) MEF cells: MICU1-KO Vivek Garg Garg et al. (2021) (Continued on next page) e2 Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER MEF cells: MICU2-KO Vivek Garg Garg et al. (2021) Experimental models: Organisms/strains C57BL/6J mouse: wild type Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000,664 Sprague-Dawley rats: wild type Charles River Laboratory Cat#001; RRID: RGD_734476 Oligonucleotides sgRNA sequence to mutate native MICU1 to C463R in HEK cells: 50-ACACCTTCCTGTGCACATTTCCACAG This paper N/A Recombinant DNA MCU, EMRE, MICU1 or MICU2 in pcDNA3.1(+) Home made Tsai et al. (2016); Tsai et al., 2017 MICU1 or MICU2 in pLJM1 This paper N/A pLKO.hygro constructs to knockdown YME1L1 or AFG3L2 Home made Tsai et al., 2017 pCMV_ABEmax Koblan et al. (2018) Addgene Cat#112095 MLM3636 sgRNA expression plasmid Keith Joung Addgene Cat#43860 Mito-GCaMP6f Timothy Ryan Ashrafi et al. (2020) Cyto-GCaMP6f Chen et al. (2013) Addgene Cat#40755 Mito-Sypher Poburko et al. (2011) Addgene Cat#48251 Cyto-Sypher Poburko et al. (2011) Addgene Cat#48250 Mito-roGFP2-Orp1 Gutscher et al. (2009) Addgene Cat#64992 Mitochondria-targeted luciferase Paolo Pinton Morciano et al. (2017) Mito-GEM-GECO1 Zhao et al. (2011) Addgene Cat#32461 MBP-MICU1 in pET24a This paper N/A MICU2 in pETDuet This paper N/A Software and algorithms Igor pro (version 8) WaveMetrics www.wavemetrics.com/products/igorpro Image Studio (version 5.2) LI-COR https://www.licor.com/bio/image-studio/ ImageJ (Mac OS X) ImageJ website https://ImageJ.nih.gov/ij Time Series Analyzer plug-in (version 3) Balaji J https://ImageJ.nih.gov/ij/plugins/time- series.html
Sample Prep:Article Title: Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MCU Cell Signaling Cat#D2Z3B; RRID: AB_2721812 EMRE Santa Cruz Cat#86337; RRID: AB_2250685 MICU1 Atlas Antibodies Cat#HPA034780; RRID: AB_10696934 MICU2 Abcam Cat#ab101465 MICU3 Atlas Antibodies Cat# HPA024771; RRID: AB_1848022 VDAC Abcam Cat# ab14734 RRID: AB_443084 COX1 Abcam Cat#ab14705; RRID: AB_2084810 COX2 Abcam Cat#ab14734 Tim23 Santa Cruz Cat#sc-5114463 FLAG Sigma-Aldrich Cat#F1804; RRID: AB_262044 YME1L1 Proteintech Cat#11510-1-AP; RRID: AB_2217459 AFG3L2 Proteintech Cat#14631-1-AP; RRID: AB_2242420 Letm1 Abcam Cat#ab55434; RRID: AB_943985 b-actin Santa Cruz Cat#sc-69879; RRID: AB_1119529 NDUFS1 Santa Cruz Cat#sc-271510; RRID: AB10655669 NDUFS3 Santa Cruz Cat#sc-374282; RRID: AB_10991315 SDHA Santa Cruz Cat#sc-390381 Rieske Santa Cruz Cat#sc-271609 RRID: AB_10655682 ATP5F1 Santa Cruz Cat#sc-514419 1D4 Home made N/A PDH-E1ɑ Santa Cruz Cat#sc-377092 RRID: AB_2716767 S293 phosphorylated PDH-E1ɑ Millipore Cat#ABS204 RRID: AB_11205754 IRDye 680RD goat-anti rabbit LI-COR Cat#925-68071; RRID: AB_2721181 IRDye 800CW goat-anti mouse LI-COR Cat#925-32210; RRID: AB_2687825 IRDye 680RD goat-anti mouse LI-COR Cat#925-68070 RRID: AB_2651128 Alkaline phosphatase conjugated anti-rabbit secondary antibody Promega Cat# S373B Bacterial and virus strains E. coli: DH5ɑ competent cells New England Biolabs Cat#C2987H E. coli: BL21(DE3) Christopher Miller Tsai et al. (2012) Biological samples Left ventricular tissues of non-failing human hearts Adult Cardiac Tissue Bank at the University of Colorado DenverAnschutz Medical campus N/A Chemicals, peptides, and recombinant proteins Lipofectamine 3000 Life Technologies Cat#L3000150 Lipofectamine 2000 Life Technologies Cat#11668019 DDM, anagrade Anatrace Cat#D310 (Continued on next page) Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RIPA buffer Santa Cruz Cat#sc-24948 Intercept blocking buffer (TBS-based) LI-COR Cat#927-60001 PVDF membranes LI-COR Cat926-31097 Protease inhibitor cocktail tablet Roche Cat#05892970001 TALON cobalt affinity resin Takara Cat#635504 CNBr-activated Sepharose 4B GE Healthcare Cat#17043001 Cycloheximide Sigma Cat#C7698 Oligomycin Cayman Cat#11342 Rotenone Cayman Cat#13995 Antimycin A Sigma Cat#A8674 Ionomycin Cayman Cat#11932 Carbachol Cayman Cat#114486 45Ca2+ radioisotope Perkin-Elmer Cat#NEZ013001MC 35S-methionine Perkin-Elmer Cat#NEG009A001MC Cysteine/methionine free medium Sigma Cat#D0422 Protein A beads Santa Cruz Cat#sc-2001 Thapsigargin Cayman Cat#10522 Digitonin Sigma-Aldrich Cat#D141 Calcium green 5N Life Technologies Cat#C3737 TMRM Invitrogen Cat#T668 FCCP Cayman Cat#15218 Doxorubicin Tokyo Chemical Industry Cat#D4193 Cisplatin Tokyo Chemical Industry Cat#D3371 Annexin V CF488A Biotium Cat#29083 Propidium Iodide Cayman Cat#14289 Hoescht 33,258 Cayman Cat#16756 Luciferin ThermoFisher Cat#PI88291 Critical commercial assays Seahorse XF Real-time ATP Rate Assay Kit Agilent Cat#103591-100 QuickChange II Kit Agilent Cat#200524 BCA assay kit Thermo Cat#23225 NativePAGE Sample Prep kit Invitrogen Cat#BN2008 NativePAGE Running Buffer kit Invitrogen Cat#BN2007 Deposited data Unprocessed images used in the figures This paper https://doi.org/10.17632/shrtrdfhyt.1 Experimental models: Cell lines HEK 293T: wild type ATCC Cat#CRL-11268; RRID: CVCL_1926 HeLa: wild type ATCC Cat#CCL-2; RRID: CVCL_0030 U2OS: wild type Cell Technologies Resource Center in the University of Colorado Anschutz Medical Campus https://medschool.cuanschutz.edu/ colorado-cancer-center/research/ shared-resources/cell-technologies/ cell-culture-services HEK 293T: MICU1-KO Home made Tsai et al. (2017) HEK 293T: MICU2-KO Home made Fan et al. (2020) HEK 293T: MICU1-MICU2-KO Home made Fan et al. (2020) HEK 239T: C463R-MICU1 (CRISPR base edited) This paper N/A MEF cells: wild type Vivek Garg Garg et al. (2021) MEF cells: MICU1-KO Vivek Garg Garg et al. (2021) (Continued on next page) e2 Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER MEF cells: MICU2-KO Vivek Garg Garg et al. (2021) Experimental models: Organisms/strains C57BL/6J mouse: wild type Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000,664 Sprague-Dawley rats: wild type Charles River Laboratory Cat#001; RRID: RGD_734476 Oligonucleotides sgRNA sequence to mutate native MICU1 to C463R in HEK cells: 50-ACACCTTCCTGTGCACATTTCCACAG This paper N/A Recombinant DNA MCU, EMRE, MICU1 or MICU2 in pcDNA3.1(+) Home made Tsai et al. (2016); Tsai et al., 2017 MICU1 or MICU2 in pLJM1 This paper N/A pLKO.hygro constructs to knockdown YME1L1 or AFG3L2 Home made Tsai et al., 2017 pCMV_ABEmax Koblan et al. (2018) Addgene Cat#112095 MLM3636 sgRNA expression plasmid Keith Joung Addgene Cat#43860 Mito-GCaMP6f Timothy Ryan Ashrafi et al. (2020) Cyto-GCaMP6f Chen et al. (2013) Addgene Cat#40755 Mito-Sypher Poburko et al. (2011) Addgene Cat#48251 Cyto-Sypher Poburko et al. (2011) Addgene Cat#48250 Mito-roGFP2-Orp1 Gutscher et al. (2009) Addgene Cat#64992 Mitochondria-targeted luciferase Paolo Pinton Morciano et al. (2017) Mito-GEM-GECO1 Zhao et al. (2011) Addgene Cat#32461 MBP-MICU1 in pET24a This paper N/A MICU2 in pETDuet This paper N/A Software and algorithms Igor pro (version 8) WaveMetrics www.wavemetrics.com/products/igorpro Image Studio (version 5.2) LI-COR https://www.licor.com/bio/image-studio/ ImageJ (Mac OS X) ImageJ website https://ImageJ.nih.gov/ij Time Series Analyzer plug-in (version 3) Balaji J https://ImageJ.nih.gov/ij/plugins/time- series.html
CRISPR:Article Title: Mechanisms and significance of tissue-specific MICU regulation of the mitochondrial calcium uniporter complex.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies MCU Cell Signaling Cat#D2Z3B; RRID: AB_2721812 EMRE Santa Cruz Cat#86337; RRID: AB_2250685 MICU1 Atlas Antibodies Cat#HPA034780; RRID: AB_10696934 MICU2 Abcam Cat#ab101465 MICU3 Atlas Antibodies Cat# HPA024771; RRID: AB_1848022 VDAC Abcam Cat# ab14734 RRID: AB_443084 COX1 Abcam Cat#ab14705; RRID: AB_2084810 COX2 Abcam Cat#ab14734 Tim23 Santa Cruz Cat#sc-5114463 FLAG Sigma-Aldrich Cat#F1804; RRID: AB_262044 YME1L1 Proteintech Cat#11510-1-AP; RRID: AB_2217459 AFG3L2 Proteintech Cat#14631-1-AP; RRID: AB_2242420 Letm1 Abcam Cat#ab55434; RRID: AB_943985 b-actin Santa Cruz Cat#sc-69879; RRID: AB_1119529 NDUFS1 Santa Cruz Cat#sc-271510; RRID: AB10655669 NDUFS3 Santa Cruz Cat#sc-374282; RRID: AB_10991315 SDHA Santa Cruz Cat#sc-390381 Rieske Santa Cruz Cat#sc-271609 RRID: AB_10655682 ATP5F1 Santa Cruz Cat#sc-514419 1D4 Home made N/A PDH-E1ɑ Santa Cruz Cat#sc-377092 RRID: AB_2716767 S293 phosphorylated PDH-E1ɑ Millipore Cat#ABS204 RRID: AB_11205754 IRDye 680RD goat-anti rabbit LI-COR Cat#925-68071; RRID: AB_2721181 IRDye 800CW goat-anti mouse LI-COR Cat#925-32210; RRID: AB_2687825 IRDye 680RD goat-anti mouse LI-COR Cat#925-68070 RRID: AB_2651128 Alkaline phosphatase conjugated anti-rabbit secondary antibody Promega Cat# S373B Bacterial and virus strains E. coli: DH5ɑ competent cells New England Biolabs Cat#C2987H E. coli: BL21(DE3) Christopher Miller Tsai et al. (2012) Biological samples Left ventricular tissues of non-failing human hearts Adult Cardiac Tissue Bank at the University of Colorado DenverAnschutz Medical campus N/A Chemicals, peptides, and recombinant proteins Lipofectamine 3000 Life Technologies Cat#L3000150 Lipofectamine 2000 Life Technologies Cat#11668019 DDM, anagrade Anatrace Cat#D310 (Continued on next page) Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER RIPA buffer Santa Cruz Cat#sc-24948 Intercept blocking buffer (TBS-based) LI-COR Cat#927-60001 PVDF membranes LI-COR Cat926-31097 Protease inhibitor cocktail tablet Roche Cat#05892970001 TALON cobalt affinity resin Takara Cat#635504 CNBr-activated Sepharose 4B GE Healthcare Cat#17043001 Cycloheximide Sigma Cat#C7698 Oligomycin Cayman Cat#11342 Rotenone Cayman Cat#13995 Antimycin A Sigma Cat#A8674 Ionomycin Cayman Cat#11932 Carbachol Cayman Cat#114486 45Ca2+ radioisotope Perkin-Elmer Cat#NEZ013001MC 35S-methionine Perkin-Elmer Cat#NEG009A001MC Cysteine/methionine free medium Sigma Cat#D0422 Protein A beads Santa Cruz Cat#sc-2001 Thapsigargin Cayman Cat#10522 Digitonin Sigma-Aldrich Cat#D141 Calcium green 5N Life Technologies Cat#C3737 TMRM Invitrogen Cat#T668 FCCP Cayman Cat#15218 Doxorubicin Tokyo Chemical Industry Cat#D4193 Cisplatin Tokyo Chemical Industry Cat#D3371 Annexin V CF488A Biotium Cat#29083 Propidium Iodide Cayman Cat#14289 Hoescht 33,258 Cayman Cat#16756 Luciferin ThermoFisher Cat#PI88291 Critical commercial assays Seahorse XF Real-time ATP Rate Assay Kit Agilent Cat#103591-100 QuickChange II Kit Agilent Cat#200524 BCA assay kit Thermo Cat#23225 NativePAGE Sample Prep kit Invitrogen Cat#BN2008 NativePAGE Running Buffer kit Invitrogen Cat#BN2007 Deposited data Unprocessed images used in the figures This paper https://doi.org/10.17632/shrtrdfhyt.1 Experimental models: Cell lines HEK 293T: wild type ATCC Cat#CRL-11268; RRID: CVCL_1926 HeLa: wild type ATCC Cat#CCL-2; RRID: CVCL_0030 U2OS: wild type Cell Technologies Resource Center in the University of Colorado Anschutz Medical Campus https://medschool.cuanschutz.edu/ colorado-cancer-center/research/ shared-resources/cell-technologies/ cell-culture-services HEK 293T: MICU1-KO Home made Tsai et al. (2017) HEK 293T: MICU2-KO Home made Fan et al. (2020) HEK 293T: MICU1-MICU2-KO Home made Fan et al. (2020) HEK 239T: C463R-MICU1 (CRISPR base edited) This paper N/A MEF cells: wild type Vivek Garg Garg et al. (2021) MEF cells: MICU1-KO Vivek Garg Garg et al. (2021) (Continued on next page) e2 Molecular Cell 82, 3661–3676.e1–e8, October 6, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER MEF cells: MICU2-KO Vivek Garg Garg et al. (2021) Experimental models: Organisms/strains C57BL/6J mouse: wild type Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000,664 Sprague-Dawley rats: wild type Charles River Laboratory Cat#001; RRID: RGD_734476 Oligonucleotides sgRNA sequence to mutate native MICU1 to C463R in HEK cells: 50-ACACCTTCCTGTGCACATTTCCACAG This paper N/A Recombinant DNA MCU, EMRE, MICU1 or MICU2 in pcDNA3.1(+) Home made Tsai et al. (2016); Tsai et al., 2017 MICU1 or MICU2 in pLJM1 This paper N/A pLKO.hygro constructs to knockdown YME1L1 or AFG3L2 Home made Tsai et al., 2017 pCMV_ABEmax Koblan et al. (2018) Addgene Cat#112095 MLM3636 sgRNA expression plasmid Keith Joung Addgene Cat#43860 Mito-GCaMP6f Timothy Ryan Ashrafi et al. (2020) Cyto-GCaMP6f Chen et al. (2013) Addgene Cat#40755 Mito-Sypher Poburko et al. (2011) Addgene Cat#48251 Cyto-Sypher Poburko et al. (2011) Addgene Cat#48250 Mito-roGFP2-Orp1 Gutscher et al. (2009) Addgene Cat#64992 Mitochondria-targeted luciferase Paolo Pinton Morciano et al. (2017) Mito-GEM-GECO1 Zhao et al. (2011) Addgene Cat#32461 MBP-MICU1 in pET24a This paper N/A MICU2 in pETDuet This paper N/A Software and algorithms Igor pro (version 8) WaveMetrics www.wavemetrics.com/products/igorpro Image Studio (version 5.2) LI-COR https://www.licor.com/bio/image-studio/ ImageJ (Mac OS X) ImageJ website https://ImageJ.nih.gov/ij Time Series Analyzer plug-in (version 3) Balaji J https://ImageJ.nih.gov/ij/plugins/time- series.html
Membrane:Article Title: Lymphatic dysfunction correlates with inflammation in the SOD1-G93A mouse model of amyotrophic lateral sclerosis.
Article Snippet: .. Blots were imaged on a LI-COR Odyssey CLx (LI-COR Biotech, Lincoln, NE), and 4x protein sample loading buffer (LI-COR cat# 928-40004), Chameleon Duo Pre-stained protein ladder (LI-COR cat# 928-60000), and low-background PVDF membrane (LI-COR cat# 926- 31097) were used as per LI-COR recommendations. .. Manufacturer instructions and reagents were followed for all steps post-transfer, including Revert 700 Total Protein Staining and Reversing (LI-COR cat# 926-11010) prior to blocking and probing.
Article Title: Lymphatic dysfunction correlates with inflammation in a mouse model of amyotrophic lateral sclerosis
Article Snippet: .. Blots were imaged on an Odyssey CLx (LI-COR, Lincoln, NE, USA), and 4× protein sample loading buffer (LI-COR, 928-40004), Chameleon Duo Pre-stained protein ladder (LI-COR, 928-60000) and low-background PVDF membrane (LI-COR, 926-31097) were used as per LI-COR recommendations. .. Manufacturer instructions and reagents were followed for all steps post-transfer, including Revert 700 Total Protein Staining and Reversing (LI-COR, 926-11010) prior to blocking and probing.
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