Irradiation:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
Control:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
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 Cat12183018A 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.
RNA Library Preparation:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
cDNA Synthesis:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
Article Title: Phosphodiesterase 3 A expression in gastrointestinal stromal tumors.
Article Snippet: .. RT‐qPCR RNA was extracted from 30 GIST and 10 liposarcoma FFPE tissue sections using QIASymphony RNA kit and QIASymphony SP instrument (Qiagen GmbH, Hilden, Germany), and 2 μL of RNA (30 to 300 ng) was reverse-transcribed into cDNA using SuperScriptTM VILOTM cDNA synthesis kit (Cat# 11754250, Thermo Ficher Scientific, Carlsbad, CA, USA) following the manufacturer’s instructions, as described earlier [12, 18]. ..
Article Title: EGR1 drives sex-differences in glioblastoma tumorigenicity
Article Snippet: The following antibodies were used: Egr1 (44D5) Rabbit mAb #4154 and Beta-actin (CST β-actin (1:5000, 8457, RRID:AB_10950489) and secondary antibodies anti-rabbit (1:2500, 7074, RRID:AB_2099233 from Cell Signaling Technologies). .. RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer instructionsRNA concentration was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and 120 ng of RNA was used to synthesize cDNA using Invitrogen’s SuperScriptTM VILOTM cDNA Synthesis Kit (ThermoFisher Scientific, 11754250). .. Quantitative RT-PCR was performed using PowerUpTM SYBRTM Green Master Mix (ThermoFisher Scientific, A25741) on the QuantStudio 3 Real-Time PCR (ThermoFisher Scientific).
Article Title: Circular RNA expression in ALS is progressively deregulated and tissue-dependent
Article Snippet: .. From each sample, 100 ng (CNS) or 200 ng (muscle) of total RNA was used as template for retro-transcription (RT) with SuperScriptTM VILOTM cDNA Synthesis Kit (Thermo Fisher Scientific), following the manufacturer’s protocol. .. Next, circRNA and mRNA levels were quantified by qPCR using PowerUp SYBR Green MasterMix (Thermo Fisher Scientific) and a set of mouse (Table ) or human (Table ) specific primers.
Article Title: Circular RNA expression in ALS is progressively deregulated and tissue-dependent.
Article Snippet: .. Data quality summary, raw counts and TPM normalized counts are given in Supplementary Material 3 and the FASTQ files are available in Gene Expression Omnibus (GSE289637). cDNA synthesis and quantitative PCR (qPCR) From each sample, 100 ng (CNS) or 200 ng (muscle) of total RNA was used as template for retro-transcription (RT) with SuperScriptTM VILOTM cDNA Synthesis Kit (Thermo Fisher Scientific), following the manufacturer’s protocol. .. Next, circRNA and mRNA levels were quantified by qPCR using PowerUp SYBR Green MasterMix (Thermo Fisher Scientific) and a set of mouse (Table S2) or human (Table S3) specific primers.
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 Cat12183018A 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.
Polymerase Chain Reaction:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
Bicinchoninic Acid Protein Assay:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
Staining:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
Imaging:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
RNA Sequencing:Article Title: The integrated stress response fine-tunes stem cell fate decisions upon serine deprivation and tissue injury.
Article Snippet: .. Fisher & Son Cat# 1817070-203 Irradiated Control AA Diet (VI, Red) Envigo TD.200483 Irradiated 2% Serine AA Diet (VI, Yellow) Envigo TD.230251 L-serine Sigma Aldrich Cat# S4500 Glycine Sigma Aldrich Cat# G7126 L-glutamine Thermo Fisher Scientific Cat# 25030081 L-asparagine Sigma A0884 GSK2656157 Cayman Chemical Cat# 17372 GCN2iB MedChemExpress HY-112654 Salubrinal Selleckchem Cat# S2923 Tunicamycin from Streptomyces sp. Sigma Aldrich T7765 Cycloheximide Sigma Aldrich C7698 L-asparaginase Biovendor RP179287010000 Sodium formate Sigma 107603 Uridine Sigma U3750 Hypoxanthine Sigma H9377 Glutathione reduced ethyl ester Sigma G1404 (±)-6-Hydroxy-2,5,7,8tetramethylchromane-2-carboxylic acid (Trolox) Sigma 238813-1G Critical commercial assays TruSeq RNA Library Preparation Kit Illumina Cat# RS-122-2001 NEBNext Ultra II DNA Library Prep kit for Illumina New England BioLabs Cat# E7645L Agencourt AMPure XP beads Beckman Coulter A63880 Direct-zol RNA Microprep Zymo Research Cat# R2062 Direct-zol RNA Miniprep Zymo Research Cat# R2050 SuperScriptTM VILOTM cDNA Synthesis Kit ThermoFisher Cat# 11754050 Power SYBRTM Green PCR Master Mix ThermoFisher Cat# 4368577 PierceTM BCA Protein Assay Kit ThermoFisher Cat# 23225 LIVE/DEAD Fixable Blue Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23105 LIVE/DEAD Fixable Red Dead Cell Stain Kit Thermo Fisher Scientific Cat# L23102 Click-iTTM EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10340 Click-iTTM Plus EdU Cell Proliferation Kit for Imaging, Alexa FluorTM 647 dye Thermo Fisher Scientific Cat# C10640 Click-iTTM Plus OPP Alexa FluorTM 647 Protein Synthesis Assay Kit Thermo Fisher Scientific Cat# C10458 ExtractaTM DNA Prep for PCR QuantaBio Cat# 97065-350 Deposited data Bulk RNA sequencing of HFSCs in telogen and anagen Wang et al. 72 GEO: GSE67404 Bulk RNA sequencing of HFSCs in telogen and anagen Gur-Cohen et al. 49 GEO: GSE123913 scRNA-seq of wound healing from Gonzales et al. 15 Gonzales et al. 15 GEO: GSE165314 Bulk RNA sequencing of HFSCs in telogen and anagen This study GEO: GSE270324 scRNA-seq of wound healing in WT and cKO HFSCs/progeny This study GEO: GSE270317 Source Data This study Data S1 Experimental models: Cell lines 293TN Producer Cell Line System Biosciences Cat# LV900A-1 (Continued on next page) e3 Cell Metabolism 37, 1–17.e1–e11, August 5, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER J2 fibroblast feeder cells Fuchs Lab N/A Primary Phgdh WT HFSCs Fuchs Lab This study Primary Phgdh cKO HFSCs Fuchs Lab This study Primary sgChr8 HFSCs Fuchs Lab This study Primary sgPsat1-A KO HFSCs Fuchs Lab This study Primary sgPsat1-B KO HFSCs Fuchs Lab This study Primary sgPsph1-A KO HFSCs Fuchs Lab This study Primary sgPsph-B KO HFSCs Fuchs Lab This study Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 000664; RRID: IMSR_JAX:000664 Mouse: CD1 Charles River #022 Mouse: Rosa26-stop-lox-stop YFP: B6.129X1-Gt(ROSA)26Sor tm1(EYFP)Cos /J The Jackson Laboratory Cat# 006148; RRID: IMSR_JAX:006148 Mouse: Sox9 tm1(cre/ERT2)Haak Akiyama Laboratory MGI:4867441 Mouse: Phgdh tm1.2Shfu Furuya and Possemato laboratories MGI:4881750 Oligonucleotides Quantitative real-time PCR primers Eurofins Please see Table S1 sgRNA oligos Eurofins Please see Table S1 Recombinant DNA pMD2.G A gift from Didier Trono Addgene plasmid #12259; RRID: Addgene_12259 psPAX2 A gift from Didier Trono Addgene plasmid #12260; RRID: Addgene_12260 LentiCRISPRv2-opti-EV Adelmann et al. 88 Addgene plasmid # 163126; RRID: Addgene_163126 LentiCRISPRv2-opti-sgChr8 This study TBD LentiCRISPRv2-opti-sgPsat1-A This study TBD LentiCRISPRv2-opti-sgPsat1-B This study TBD LentiCRISPRv2-opti-sgPsph-A This study TBD LentiCRISPRv2-opti-sgPsph-B This study TBD Software and algorithms Graphpad Prism https://www.graphpad.com/ scientific-software/prism/ N/A ImageJ/Fiji Schneider et al. 89 https://imagej.nih.gov/ij/ Flowjo https://www.flowjo.com N/A Adobe Photoshop Adobe.com N/A Adobe Illustrator CS5 Adobe.com N/A R https://www.r-project.org/ N/A RStudio https://posit.co/products/ open-source/rstudio/ N/A TxDb.Mmusculus.
Formalin-fixed Paraffin-Embedded:Article Title: Phosphodiesterase 3 A expression in gastrointestinal stromal tumors.
Article Snippet: .. RT‐qPCR RNA was extracted from 30 GIST and 10 liposarcoma FFPE tissue sections using QIASymphony RNA kit and QIASymphony SP instrument (Qiagen GmbH, Hilden, Germany), and 2 μL of RNA (30 to 300 ng) was reverse-transcribed into cDNA using SuperScriptTM VILOTM cDNA synthesis kit (Cat# 11754250, Thermo Ficher Scientific, Carlsbad, CA, USA) following the manufacturer’s instructions, as described earlier [12, 18]. ..
Reverse Transcription:Article Title: Phosphodiesterase 3 A expression in gastrointestinal stromal tumors.
Article Snippet: .. RT‐qPCR RNA was extracted from 30 GIST and 10 liposarcoma FFPE tissue sections using QIASymphony RNA kit and QIASymphony SP instrument (Qiagen GmbH, Hilden, Germany), and 2 μL of RNA (30 to 300 ng) was reverse-transcribed into cDNA using SuperScriptTM VILOTM cDNA synthesis kit (Cat# 11754250, Thermo Ficher Scientific, Carlsbad, CA, USA) following the manufacturer’s instructions, as described earlier [12, 18]. ..
Isolation:Article Title: EGR1 drives sex-differences in glioblastoma tumorigenicity
Article Snippet: The following antibodies were used: Egr1 (44D5) Rabbit mAb #4154 and Beta-actin (CST β-actin (1:5000, 8457, RRID:AB_10950489) and secondary antibodies anti-rabbit (1:2500, 7074, RRID:AB_2099233 from Cell Signaling Technologies). .. RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer instructionsRNA concentration was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and 120 ng of RNA was used to synthesize cDNA using Invitrogen’s SuperScriptTM VILOTM cDNA Synthesis Kit (ThermoFisher Scientific, 11754250). .. Quantitative RT-PCR was performed using PowerUpTM SYBRTM Green Master Mix (ThermoFisher Scientific, A25741) on the QuantStudio 3 Real-Time PCR (ThermoFisher Scientific).
Concentration Assay:Article Title: EGR1 drives sex-differences in glioblastoma tumorigenicity
Article Snippet: The following antibodies were used: Egr1 (44D5) Rabbit mAb #4154 and Beta-actin (CST β-actin (1:5000, 8457, RRID:AB_10950489) and secondary antibodies anti-rabbit (1:2500, 7074, RRID:AB_2099233 from Cell Signaling Technologies). .. RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer instructionsRNA concentration was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and 120 ng of RNA was used to synthesize cDNA using Invitrogen’s SuperScriptTM VILOTM cDNA Synthesis Kit (ThermoFisher Scientific, 11754250). .. Quantitative RT-PCR was performed using PowerUpTM SYBRTM Green Master Mix (ThermoFisher Scientific, A25741) on the QuantStudio 3 Real-Time PCR (ThermoFisher Scientific).
Spectrophotometry:Article Title: EGR1 drives sex-differences in glioblastoma tumorigenicity
Article Snippet: The following antibodies were used: Egr1 (44D5) Rabbit mAb #4154 and Beta-actin (CST β-actin (1:5000, 8457, RRID:AB_10950489) and secondary antibodies anti-rabbit (1:2500, 7074, RRID:AB_2099233 from Cell Signaling Technologies). .. RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer instructionsRNA concentration was quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and 120 ng of RNA was used to synthesize cDNA using Invitrogen’s SuperScriptTM VILOTM cDNA Synthesis Kit (ThermoFisher Scientific, 11754250). .. Quantitative RT-PCR was performed using PowerUpTM SYBRTM Green Master Mix (ThermoFisher Scientific, A25741) on the QuantStudio 3 Real-Time PCR (ThermoFisher Scientific).
Incubation:
Gene Expression:Article Title: Circular RNA expression in ALS is progressively deregulated and tissue-dependent.
Article Snippet: .. Data quality summary, raw counts and TPM normalized counts are given in Supplementary Material 3 and the FASTQ files are available in Gene Expression Omnibus (GSE289637). cDNA synthesis and quantitative PCR (qPCR) From each sample, 100 ng (CNS) or 200 ng (muscle) of total RNA was used as template for retro-transcription (RT) with SuperScriptTM VILOTM cDNA Synthesis Kit (Thermo Fisher Scientific), following the manufacturer’s protocol. .. Next, circRNA and mRNA levels were quantified by qPCR using PowerUp SYBR Green MasterMix (Thermo Fisher Scientific) and a set of mouse (Table S2) or human (Table S3) specific primers.
Real-time Polymerase Chain Reaction:Article Title: Circular RNA expression in ALS is progressively deregulated and tissue-dependent.
Article Snippet: .. Data quality summary, raw counts and TPM normalized counts are given in Supplementary Material 3 and the FASTQ files are available in Gene Expression Omnibus (GSE289637). cDNA synthesis and quantitative PCR (qPCR) From each sample, 100 ng (CNS) or 200 ng (muscle) of total RNA was used as template for retro-transcription (RT) with SuperScriptTM VILOTM cDNA Synthesis Kit (Thermo Fisher Scientific), following the manufacturer’s protocol. .. Next, circRNA and mRNA levels were quantified by qPCR using PowerUp SYBR Green MasterMix (Thermo Fisher Scientific) and a set of mouse (Table S2) or human (Table S3) specific primers.
Synthesized:
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 Cat12183018A 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 Cat12183018A 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 Cat12183018A 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 Cat12183018A 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 Cat12183018A 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.
Multiplex 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 Cat12183018A 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 Cat12183018A 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 Cat12183018A 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.
|
Thermo Fisher is a verified supplier 
Thermo Fisher manufactures this product 