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snapshot multiplex kit  (Thermo Fisher)


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    Thermo Fisher snapshot multiplex kit
    Snapshot Multiplex Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/snapshot+multiplex+kit/snapshot+multiplex+kit/pmc10897523__mmc2-662-171-174
    Average 90 stars, based on 1 article reviews
    snapshot multiplex kit - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Multiplex Assay:

    Article Title: The Impact of CYP2D6 Metabolizer Phenotypes on the EDDP/Methadone Metabolic Ratio: A Comprehensive Analysis
    Article Snippet: Methadone is a synthetic opioid that is often used for prevention of withdrawal symptoms and for management of chronic pain.. In concentrations above the therapeutic level however, methadone can lead to detrimental side effects, such as respiratory depression.. Several cytochrome P450 (CYP) enzymes are involved in methadone metabolism, foremost in building the main metabolite 2-ethylidene1,5-dimethyl-3,3diphenylpyrrolidine (EDDP).

    Article Title: Influence of Genetic Polymorphisms and Biochemical Biomarkers on Response to Nutritional Iron Supplementation and Performance in a Professional Football Team: A Pilot Longitudinal Study
    Article Snippet: .. Genotyping was conducted using single-nucleotide primer extension (SNPE) with the SNaPshot Multiplex Kit (Thermo Fisher Scientific, Waltham, MA, USA), and results were analyzed via capillary electrophoresis on an ABI3500 instrument (Applied Biosystems, Foster City, CA, USA). .. The bioinformatic interpretation was performed using GeneMapper 5.0 software (Applied Biosystems, Foster City, CA, USA).

    Article Title: Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility
    Article Snippet: A segment of DNA surrounding the SNPs was amplified by PCR using Takara HotStarTaq (Takara). .. After purification using shrimp alkaline phosphatase and exonuclease I (Epicentre), the PCR products were subjected to a primer extension assay using a SNaPshot Multiplex Kit (ABI). .. The resulting primer extension products were analysed on an ABI 3130xl capillary electrophoresis DNA instrument using Gene Mapper 4.1 software (Applied Biosystems, Foster City, CA).

    Article Title: A Ge.F.I. Collaborative Study: Evaluating Reproducibility and Accuracy of a DNA-Methylation-Based Age-Predictive Assay for Routine Implementation in Forensic Casework.
    Article Snippet: PCR amplification was followed by an enzymatic clean-up with the ExoSAP Express PCR Product Cleanup reagent (Applied Biosystems, Waltham, MA, USA) [44]. .. The multiplex SBE reaction was performed using the SNaPshot Multiplex Kit (Applied Biosystems, Waltham, MA, USA). ..

    Article Title: Genetic characterization of phenotypic traits in endangered Taishu horse breed and their breeding strategy.
    Article Snippet: In brief, multiplex PCR was carried out in a total volume of 15 μL with approximately 20 ng genomic DNA, 0.33 μM of each primer, 2.5 mM MgCl2, 0.33 mM dNTPs, 10× reaction buffer, and 0.5 U of AmpliTaq Gold (Thermo Fisher Scientific) under the following thermal conditions: an initial incubation at 95 °C for 10 min; 30 cycles at 95 °C for 30 s, 60 °C for 1 min, and 72 °C for 30 s; and a final incubation at 72 °C for 10 min. .. The PCR product purified using ExoSAP-IT (Thermo Fisher Scientific) was subjected to SNV genotyping using the SNaPshot Multiplex Kit (Thermo Fisher Scientific) with 0.02–0.1 μM of the primers (Table 2). .. SNVs of MSTN, LCORL, and DMRT3 and an INDEL of MSTN were genotyped using the TaqMan SNP genotyping assay (Thermo Fisher Scientific) based on Saito et al. [18].

    Article Title: The association of HIF1A gene polymorphism and its expression with ischemic stroke
    Article Snippet: .. Genotyping was performed using ABI SNaPshot Multiplex Kit, the procedure is as follows: DNA was amplified by Multiplex PCR, then single-base extension reactions were performed. .. The extension products were denatured with Hi-Di formamide, then the products were separated and analyzed using ABI 3730xl genetic analyzer by capillary electrophoresis method.

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    Article Title: A Single Multiplex PCR and Single-Nucleotide Extension Assay for the Detection of Common Thanatophoric Dysplasia I and II Mutations.
    Article Snippet: opyright a 2024 Association for Molecular P nd data mining, AI training, and similar tech ttps://doi.org/10.1016/j.jmoldx.2024.08.008 Mutation analysis provides confirmation of a clinical and radiological diagnosis of thanatophoric dysplasia types I and II (TD I and II).. We developed a single multiplexed PCR and a single-nucleotide extension (SNE) assay to identify 14 common mutations causing 99% of TD I and TD II, including the challenging three adjacent mutations in the stop codon of exon 18 of the FGFR3 gene.. The assay design also provides a solution for resolving SNE PCR product sizing using performance optimized polymer-7.

    Electrophoresis:

    Article Title: Influence of Genetic Polymorphisms and Biochemical Biomarkers on Response to Nutritional Iron Supplementation and Performance in a Professional Football Team: A Pilot Longitudinal Study
    Article Snippet: .. Genotyping was conducted using single-nucleotide primer extension (SNPE) with the SNaPshot Multiplex Kit (Thermo Fisher Scientific, Waltham, MA, USA), and results were analyzed via capillary electrophoresis on an ABI3500 instrument (Applied Biosystems, Foster City, CA, USA). .. The bioinformatic interpretation was performed using GeneMapper 5.0 software (Applied Biosystems, Foster City, CA, USA).

    Purification:

    Article Title: Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility
    Article Snippet: A segment of DNA surrounding the SNPs was amplified by PCR using Takara HotStarTaq (Takara). .. After purification using shrimp alkaline phosphatase and exonuclease I (Epicentre), the PCR products were subjected to a primer extension assay using a SNaPshot Multiplex Kit (ABI). .. The resulting primer extension products were analysed on an ABI 3130xl capillary electrophoresis DNA instrument using Gene Mapper 4.1 software (Applied Biosystems, Foster City, CA).

    Article Title: Genetic characterization of phenotypic traits in endangered Taishu horse breed and their breeding strategy.
    Article Snippet: In brief, multiplex PCR was carried out in a total volume of 15 μL with approximately 20 ng genomic DNA, 0.33 μM of each primer, 2.5 mM MgCl2, 0.33 mM dNTPs, 10× reaction buffer, and 0.5 U of AmpliTaq Gold (Thermo Fisher Scientific) under the following thermal conditions: an initial incubation at 95 °C for 10 min; 30 cycles at 95 °C for 30 s, 60 °C for 1 min, and 72 °C for 30 s; and a final incubation at 72 °C for 10 min. .. The PCR product purified using ExoSAP-IT (Thermo Fisher Scientific) was subjected to SNV genotyping using the SNaPshot Multiplex Kit (Thermo Fisher Scientific) with 0.02–0.1 μM of the primers (Table 2). .. SNVs of MSTN, LCORL, and DMRT3 and an INDEL of MSTN were genotyped using the TaqMan SNP genotyping assay (Thermo Fisher Scientific) based on Saito et al. [18].

    Polymerase Chain Reaction:

    Article Title: Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility
    Article Snippet: A segment of DNA surrounding the SNPs was amplified by PCR using Takara HotStarTaq (Takara). .. After purification using shrimp alkaline phosphatase and exonuclease I (Epicentre), the PCR products were subjected to a primer extension assay using a SNaPshot Multiplex Kit (ABI). .. The resulting primer extension products were analysed on an ABI 3130xl capillary electrophoresis DNA instrument using Gene Mapper 4.1 software (Applied Biosystems, Foster City, CA).

    Article Title: Genetic characterization of phenotypic traits in endangered Taishu horse breed and their breeding strategy.
    Article Snippet: In brief, multiplex PCR was carried out in a total volume of 15 μL with approximately 20 ng genomic DNA, 0.33 μM of each primer, 2.5 mM MgCl2, 0.33 mM dNTPs, 10× reaction buffer, and 0.5 U of AmpliTaq Gold (Thermo Fisher Scientific) under the following thermal conditions: an initial incubation at 95 °C for 10 min; 30 cycles at 95 °C for 30 s, 60 °C for 1 min, and 72 °C for 30 s; and a final incubation at 72 °C for 10 min. .. The PCR product purified using ExoSAP-IT (Thermo Fisher Scientific) was subjected to SNV genotyping using the SNaPshot Multiplex Kit (Thermo Fisher Scientific) with 0.02–0.1 μM of the primers (Table 2). .. SNVs of MSTN, LCORL, and DMRT3 and an INDEL of MSTN were genotyped using the TaqMan SNP genotyping assay (Thermo Fisher Scientific) based on Saito et al. [18].

    Article Title: The association of HIF1A gene polymorphism and its expression with ischemic stroke
    Article Snippet: .. Genotyping was performed using ABI SNaPshot Multiplex Kit, the procedure is as follows: DNA was amplified by Multiplex PCR, then single-base extension reactions were performed. .. The extension products were denatured with Hi-Di formamide, then the products were separated and analyzed using ABI 3730xl genetic analyzer by capillary electrophoresis method.

    Primer Extension Assay:

    Article Title: Identification and validation of lncRNA mutation hotspot SNPs associated with myasthenia gravis susceptibility
    Article Snippet: A segment of DNA surrounding the SNPs was amplified by PCR using Takara HotStarTaq (Takara). .. After purification using shrimp alkaline phosphatase and exonuclease I (Epicentre), the PCR products were subjected to a primer extension assay using a SNaPshot Multiplex Kit (ABI). .. The resulting primer extension products were analysed on an ABI 3130xl capillary electrophoresis DNA instrument using Gene Mapper 4.1 software (Applied Biosystems, Foster City, CA).

    Amplification:

    Article Title: The association of HIF1A gene polymorphism and its expression with ischemic stroke
    Article Snippet: .. Genotyping was performed using ABI SNaPshot Multiplex Kit, the procedure is as follows: DNA was amplified by Multiplex PCR, then single-base extension reactions were performed. .. The extension products were denatured with Hi-Di formamide, then the products were separated and analyzed using ABI 3730xl genetic analyzer by capillary electrophoresis method.

    Recombinant:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    Sulforhodamine B Assay:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    CyQUANT Assay:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    Proliferation Assay:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    DNA Library Preparation:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    cDNA Synthesis:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    SYBR Green Assay:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    Control:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    Mutagenesis:

    Article Title: Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-NQO1 Thermo fisher Scientific Cat#39–3700, clone A180; RRID: AB_2533410 Anti-ACTIN Sigma-Aldrich Cat#SAB5500001, clone SP124 Anti-GAPDH Sigma-Aldrich Cat#G8795; RRID:AB_1078991 Rabbit anti-MAP2 Cell Signaling Technology Cat# 4542, RRID:AB_10693782 Rabbit anti-bIIITUBULIN Cell Signaling Technology Cat# 5568, RRID:AB_10694505 Mouse anti-GFAP Millipore Cat# MAB360, RRID:AB_11212597 Goat anti-Rabbit IgG Alexa Fluor 488 Thermo Fisher Scientific Cat# A-11034, RRID:AB_2576217 Goat anti-Mouse IgG Alexa Fluor 546 Thermo Fisher Scientific Cat# A-11030, RRID:AB_2534089 Hoechst 33342 Invitrogen Cat#H1399 Chemicals, peptides, and recombinant proteins Idebenone Santhera Pharmaceuticals Gift H2DCFDA Thermo fisher Scientific Cat#D399 Sulforhodamine B (SRB) Merck Cat#S1402 Dicoumarol Sigma-Aldrich 287897 N-acetyl-cysteine (NAC) Sigma-Aldrich A7250 Critical commercial assays Seahorse XFe Cell Mito Stress Test Kit Seahorse Bioscience Cat#102340-100 Seahorse XFe96 FluxPak mini Seahorse Bioscience Cat#102601-100 XF medium pH 7.4 Seahorse Bioscience Cat#103575-100 CyQuant Direct Cell Proliferation Assay Kit Life Technologies Cat#C35011 Lentiviral Packaging Kit Origene Cat#TR30037 Nextera XT DNA Library Preparation Kit (96 samples) Illumina Cat#FC-131-1096 Nextera XT Index Kit v2 Set A (96 indexes, 384 samples) Illumina Cat#FC-131-2001 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 SNaPshot Multiplex Kit Applied Biosystems Cat#4323159 NucleoSpin Tissue, Mini kit for DNA MACHEREY-NAGEL Cat#740952 Qubit 1X dsDNA HS Assay Kit Invitrogen Cat#Q33231 SureSelect Human All Exon V5/V6 kits Agilent Technologies Cat#5190-8863 Pure Link RNA mini kit Thermo Fisher Scientific Cat#12183018A SuperScriptTM VILOTM cDNA Synthesis Kit Thermo Fisher Scientific Cat#11754050 LightCycler 480 SYBR Green I Roche Cat# 04887352001 Deposited data Human reference genome NCBI build 37, GRCh37 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/ genome/assembly/grc/human/ Genome Aggregation Database (gnomAD) v2.1.1 Broad Institute http://gnomad.broadinstitute.org/; RRID:SCR_014964 Experimental models: Cell lines Skin fibroblasts (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper N/A Wild-type and 3460/ND1 cybrids This paper, Strobe et al.,65 and Ghelli et al.66 N/A (Continued on next page) Cell Reports Medicine 5, 101383, February 20, 2024 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Neural precursors cells (control, carrying the 3460/ND1 or the 11778/ND4 mutation) This paper and Peron et al.45 N/A Oligonucleotides Primers for qPCR This paper See supplemental information Primers for NQO1 sequencing This paper See supplemental information Primers for NQO1 SNaPshot assay This paper See supplemental information Recombinant DNA pLenti-C-Myc-DDK-P2A-Puro Origene Plasmid #PS100092 human NQO1 isoform 1 in pLenti-CMyc-DDK-P2A-Puro Origene Plasmid #RC200620L3 Software and algorithms ANNOVAR Wang et al.67 https://annovar.openbioinformatics. org/en/latest/; RRID:SCR_012821 bcl2fastq v2.20 Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl2fastq-conversion-software.html; RRID:SCR_015058 Burrows-Wheeler Aligner v0.7.17 Li and Durbin68 http://bio-bwa.sourceforge.net/; RRID:SCR_010910 GeneMapper Software v4.1 Applied Biosystems RRID:SCR_014290 Genome Analysis Toolkit v3.8 Van der Auwera GA, O’Connor BD.

    Article Title: A Single Multiplex PCR and Single-Nucleotide Extension Assay for the Detection of Common Thanatophoric Dysplasia I and II Mutations.
    Article Snippet: opyright a 2024 Association for Molecular P nd data mining, AI training, and similar tech ttps://doi.org/10.1016/j.jmoldx.2024.08.008 Mutation analysis provides confirmation of a clinical and radiological diagnosis of thanatophoric dysplasia types I and II (TD I and II).. We developed a single multiplexed PCR and a single-nucleotide extension (SNE) assay to identify 14 common mutations causing 99% of TD I and TD II, including the challenging three adjacent mutations in the stop codon of exon 18 of the FGFR3 gene.. The assay design also provides a solution for resolving SNE PCR product sizing using performance optimized polymer-7.

    Labeling:

    Article Title: A Single Multiplex PCR and Single-Nucleotide Extension Assay for the Detection of Common Thanatophoric Dysplasia I and II Mutations.
    Article Snippet: opyright a 2024 Association for Molecular P nd data mining, AI training, and similar tech ttps://doi.org/10.1016/j.jmoldx.2024.08.008 Mutation analysis provides confirmation of a clinical and radiological diagnosis of thanatophoric dysplasia types I and II (TD I and II).. We developed a single multiplexed PCR and a single-nucleotide extension (SNE) assay to identify 14 common mutations causing 99% of TD I and TD II, including the challenging three adjacent mutations in the stop codon of exon 18 of the FGFR3 gene.. The assay design also provides a solution for resolving SNE PCR product sizing using performance optimized polymer-7.

    Polymer:

    Article Title: A Single Multiplex PCR and Single-Nucleotide Extension Assay for the Detection of Common Thanatophoric Dysplasia I and II Mutations.
    Article Snippet: opyright a 2024 Association for Molecular P nd data mining, AI training, and similar tech ttps://doi.org/10.1016/j.jmoldx.2024.08.008 Mutation analysis provides confirmation of a clinical and radiological diagnosis of thanatophoric dysplasia types I and II (TD I and II).. We developed a single multiplexed PCR and a single-nucleotide extension (SNE) assay to identify 14 common mutations causing 99% of TD I and TD II, including the challenging three adjacent mutations in the stop codon of exon 18 of the FGFR3 gene.. The assay design also provides a solution for resolving SNE PCR product sizing using performance optimized polymer-7.



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