other:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Article Title: IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes Tumor Progression.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER GSVA http://bioconductor.org v1.32.0 Hmisc https://cran.r-project.org v4.2-0 Image Lab software 6.0.1 Bio-Rad https://www.bio-rad.com/de-de/product/ image-lab-software?ID=KRE6P5E8Z JCoRe https://github.com/ JULIELab/jcore-base v2.4 Limma http://bioconductor.org v3.40.6 and v3.42.2 Lumi http://bioconductor.org v2.36.0 MassHunter B06.00 or B10.00 software packages Agilent https://www.agilent.com/en/products/software- informatics/mass-spectrometry-software MassLynx 4.1 Software Waters https://www.waters.com/waters/en_US/MassLynx- MS-Software/nav.htm?cid=513662&locale=en_US MOFA http://bioconductor.org v1.0.0 mogene20sttranscriptcluster.db http://bioconductor.org v8.7.0 NIS Elements software version 4.13.04 Nikon https://www.microscope.healthcare.nikon. com/de_EU/products/software/nis-elements Oligo http://bioconductor.org v1.48.0 org.Hs.eg.db http://bioconductor.org v3.8.2 pd.hugene.2.0.st http://bioconductor.org v3.14.1 Progenesis QI Software Waters https://www.waters.com/waters/en_US/ Progenesis-QI-Software/nav.htm?cid= 134790655&lset=1&locale=en_ US&changedCountry=Y QuantAnalysis Bruker Daltonik v4.3 (Build 110.102.1532) R https://cran.r-project.org v3.6 RColorBrewer https://cran.r-project.org v1.1-2 StepOne Software v2.3 Thermo Fisher Scientific https://www.thermofisher.com/us/en/home/ technical-resources/software-downloads/ StepOne-and-StepOnePlus-Real-Time-PCRSystem.html SummarizedExperiment http://bioconductor.org v1.14.1 Survival https://cran.r-project.org v2.44-1.1 Survminer https://cran.r-project.org v0.4.5 TCGAbiolinks https://github.com/ BioinformaticsFMRP/ TCGAbiolinks v2.9.5 TScratch 1.0 Gebäck et al., 2009 https://github.com/cselab/TScratch UNIFI 1.8.2 Waters https://www.waters.com/waters/en_US/ UNIFI-Scientific-Information-System/ nav.htm?locale=en_US&cid=134801648 WGCNA https://cran.r-project.org v1.66 Other 0.45 mm pore filter Merck Millipore Catt# SLHA033SS 2-well cell culture inserts ibidi Cat# 80209 6 cm cell culture dish Greiner bio-one Cat# 628160 6-well plates TPP Cat# 92006 10 cm cell culture dish TPP Cat# 93100 24-well plates TPP Cat# 92424 70 mm cell strainers BD Biosciences Cat# 352350 96-well tissue culture test plates TPP Cat# 92696 Amicon Ultra-2 mL 30K Centrifugal Filter Units Merck Millipore Cat# UFC203024 (Continued on next page) ll OPEN ACCESS Cell 182, 1252–1270.e1–e20, September 3, 2020 e7 Article
Magnetic Beads:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER HA peptide ThermoFisher Scientific Cat# 26184 Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-DYKDDDDK Tag (L5) Affinity Gel BioLegend Cat# 651503 Anti-c-Myc Tag (9E10) Affinity Gel BioLegend Cat# 658502 Ni-NTA His,Bind Resin EMD Millipore Cat# 70666 Phosphatidylinositol 3,4,5-trisphosphate diC8 (diC8-PI [3,4,5]P3) Echelon Biosciences, Inc. Cat# P-3908 [g-32P]-ATP MP Biochemicals Cat# 0135001 [8-14C]-ADP Perkin Elmer Cat# 0113004 D-[5-3H]-glucose Perkin Elmer Cat# NET53100 13C6-glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396 13C5-glutamine Cambridge Isotope Laboratories, Inc. Cat# CLM-1822 LY294002 Selleck Chemicals Cat# S1105 MK-2206 Selleck Chemicals Cat# S1078 Critical Commercial Assays ATP Colorimetric/Fluorometric Assay Kit BioVision Cat# K354-100 L-Lactate Assay Kit II Eton Bioscience Cat# 120005 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 Tumor Dissociation Kit, mouse Miltenyi Biotec Inc. Cat# 130-096-730 VECTASTAIN Elite ABC HRP Kit Vector Laboratories Cat# PK-6101 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 Seahorse XF Analyzer Agilent Technologies N/A Malachite Green Assay Kit Echelon Biosciences Inc Cat# K-1500 SensoLyte FDP Protein Phosphatase Assay Kit AnaSpec Co Cat# AS-71100 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Deposited Data Raw Data This paper, Mendeley Data https://data.mendeley.com/datasets/ 3s8ny9vh85/draft?a=2b486ba9-a27745a6-bfb7-546f806deb7a Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: A172 ATCC Cat# CRL-1620 Human: LN229 ATCC Cat# CRL-2611 Human: LN18 ATCC Cat# CRL-2610 Human: HEK293T ATCC Cat# CRL-11268 Mouse: Pten+/+ MEFs Wang et al., 2011 N/A Mouse: Pten / MEFs Wang et al., 2011 N/A Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas N/A MD Anderson Cancer Center Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides PGK1 pY324 peptide (318-PESSKK-pY-AEAVTR-330) This paper, synthesized by Selleck Chemicals N/A acidic standard PTEN substrate peptide poly-(EY) (RRREEEpYEEE) This paper, synthesized by Selleck Chemicals N/A Primers used in this paper, see Table S3 This paper N/A (Continued on next page) e2 Molecular Cell 76, 1–12.e1–e7, November 7, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
Mutagenesis:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER HA peptide ThermoFisher Scientific Cat# 26184 Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-DYKDDDDK Tag (L5) Affinity Gel BioLegend Cat# 651503 Anti-c-Myc Tag (9E10) Affinity Gel BioLegend Cat# 658502 Ni-NTA His,Bind Resin EMD Millipore Cat# 70666 Phosphatidylinositol 3,4,5-trisphosphate diC8 (diC8-PI [3,4,5]P3) Echelon Biosciences, Inc. Cat# P-3908 [g-32P]-ATP MP Biochemicals Cat# 0135001 [8-14C]-ADP Perkin Elmer Cat# 0113004 D-[5-3H]-glucose Perkin Elmer Cat# NET53100 13C6-glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396 13C5-glutamine Cambridge Isotope Laboratories, Inc. Cat# CLM-1822 LY294002 Selleck Chemicals Cat# S1105 MK-2206 Selleck Chemicals Cat# S1078 Critical Commercial Assays ATP Colorimetric/Fluorometric Assay Kit BioVision Cat# K354-100 L-Lactate Assay Kit II Eton Bioscience Cat# 120005 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 Tumor Dissociation Kit, mouse Miltenyi Biotec Inc. Cat# 130-096-730 VECTASTAIN Elite ABC HRP Kit Vector Laboratories Cat# PK-6101 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 Seahorse XF Analyzer Agilent Technologies N/A Malachite Green Assay Kit Echelon Biosciences Inc Cat# K-1500 SensoLyte FDP Protein Phosphatase Assay Kit AnaSpec Co Cat# AS-71100 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Deposited Data Raw Data This paper, Mendeley Data https://data.mendeley.com/datasets/ 3s8ny9vh85/draft?a=2b486ba9-a27745a6-bfb7-546f806deb7a Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: A172 ATCC Cat# CRL-1620 Human: LN229 ATCC Cat# CRL-2611 Human: LN18 ATCC Cat# CRL-2610 Human: HEK293T ATCC Cat# CRL-11268 Mouse: Pten+/+ MEFs Wang et al., 2011 N/A Mouse: Pten / MEFs Wang et al., 2011 N/A Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas N/A MD Anderson Cancer Center Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides PGK1 pY324 peptide (318-PESSKK-pY-AEAVTR-330) This paper, synthesized by Selleck Chemicals N/A acidic standard PTEN substrate peptide poly-(EY) (RRREEEpYEEE) This paper, synthesized by Selleck Chemicals N/A Primers used in this paper, see Table S3 This paper N/A (Continued on next page) e2 Molecular Cell 76, 1–12.e1–e7, November 7, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
Article Title: Small-molecule inhibitors of the protein kinase DYRK as potential therapeutic candidates in cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYRK1A Santa Cruz Cat# sc-100376; RRID: AB_1122375 EGFR Santa Cruz Cat# sc-373746; RRID: AB_10920395 GAPDH Santa Cruz Cat# sc-47724; RRID: AB_627678 pERK Cell Signaling Cat# 9101; RRID: AB_331646 ERK Santa Cruz Cat# sc-514302; RRID: AB_2571739 HA antibody GenScript Cat# A01621; RRID: AB_2622159 c-Cbl Cell Signaling Cat# 2747; RRID: AB_2275284 DYRK2 Santa Cruz Cat# sc-293487 DYRK3 Santa Cruz Cat# sc-390532 HRP goat anti-mouse Abcam Cat# ab6789; RRID: AB_955439 HRP goat anti-rabbit Abcam Cat# ab6721; RRID: AB_955447 Sprouty2 Santa Cruz Cat# sc-518014 Bacterial and virus strains One ShotTM BL21(DE3) Chemically Competent E. coli Thermo Fisher Cat# C600003 Rosetta (DE3) Competent Cells - Novagen Millipore Sigma Cat# 70954-3 One ShotTM Stbl3TM Chemically Competent E. coli Thermo Fisher Cat# C737303 Chemicals, peptides, and recombinant proteins MG132 Sigma Cat# M8699 Bafilomycin A1 (BaFA1) Tocris Bioscience Cat# 1334 B-27 Supplement minus Vitamin-A Invitrogen Cat# 12587010 Human EGF Fujifilm Biosciences Cat# 100-26 Human FGF-2 Fujifilm Biosciences Cat# 100-28 Human PGDF-AA Fujifilm Biosciences Cat# 100-16 Human PGDF-BB Fujifilm Biosciences Cat# 100-18 Heparin StemCell Technologies Cat# 07980 Critical commercial assays ADP-Glo Kinase assay kit Promega Cat# V6930 PierceTM BCA Protein Assay kit Thermo Fisher Cat# 23225 Quik Change II Site-directed Mutagenesis kit Agilent technologies Cat# 200523 Deposited data DYRK1A – FC-3 crystal structure This paper PDB ID: 9YKO https://www.rcsb.org/ structure/9YKO Experimental models: Cell lines Human: U87MG cells ATCC Cat# HTB-14 Human: LN229 cells ATCC Cat# CRL-2611 (Continued on next page) ll OPEN ACCESS Article e1 Cell Chemical Biology 33, 1–13.e1–e7, June 18, 2026 ..
Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Malachite Green Assay:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER HA peptide ThermoFisher Scientific Cat# 26184 Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-DYKDDDDK Tag (L5) Affinity Gel BioLegend Cat# 651503 Anti-c-Myc Tag (9E10) Affinity Gel BioLegend Cat# 658502 Ni-NTA His,Bind Resin EMD Millipore Cat# 70666 Phosphatidylinositol 3,4,5-trisphosphate diC8 (diC8-PI [3,4,5]P3) Echelon Biosciences, Inc. Cat# P-3908 [g-32P]-ATP MP Biochemicals Cat# 0135001 [8-14C]-ADP Perkin Elmer Cat# 0113004 D-[5-3H]-glucose Perkin Elmer Cat# NET53100 13C6-glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396 13C5-glutamine Cambridge Isotope Laboratories, Inc. Cat# CLM-1822 LY294002 Selleck Chemicals Cat# S1105 MK-2206 Selleck Chemicals Cat# S1078 Critical Commercial Assays ATP Colorimetric/Fluorometric Assay Kit BioVision Cat# K354-100 L-Lactate Assay Kit II Eton Bioscience Cat# 120005 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 Tumor Dissociation Kit, mouse Miltenyi Biotec Inc. Cat# 130-096-730 VECTASTAIN Elite ABC HRP Kit Vector Laboratories Cat# PK-6101 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 Seahorse XF Analyzer Agilent Technologies N/A Malachite Green Assay Kit Echelon Biosciences Inc Cat# K-1500 SensoLyte FDP Protein Phosphatase Assay Kit AnaSpec Co Cat# AS-71100 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Deposited Data Raw Data This paper, Mendeley Data https://data.mendeley.com/datasets/ 3s8ny9vh85/draft?a=2b486ba9-a27745a6-bfb7-546f806deb7a Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: A172 ATCC Cat# CRL-1620 Human: LN229 ATCC Cat# CRL-2611 Human: LN18 ATCC Cat# CRL-2610 Human: HEK293T ATCC Cat# CRL-11268 Mouse: Pten+/+ MEFs Wang et al., 2011 N/A Mouse: Pten / MEFs Wang et al., 2011 N/A Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas N/A MD Anderson Cancer Center Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides PGK1 pY324 peptide (318-PESSKK-pY-AEAVTR-330) This paper, synthesized by Selleck Chemicals N/A acidic standard PTEN substrate peptide poly-(EY) (RRREEEpYEEE) This paper, synthesized by Selleck Chemicals N/A Primers used in this paper, see Table S3 This paper N/A (Continued on next page) e2 Molecular Cell 76, 1–12.e1–e7, November 7, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
Phosphatase Assay:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER HA peptide ThermoFisher Scientific Cat# 26184 Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-DYKDDDDK Tag (L5) Affinity Gel BioLegend Cat# 651503 Anti-c-Myc Tag (9E10) Affinity Gel BioLegend Cat# 658502 Ni-NTA His,Bind Resin EMD Millipore Cat# 70666 Phosphatidylinositol 3,4,5-trisphosphate diC8 (diC8-PI [3,4,5]P3) Echelon Biosciences, Inc. Cat# P-3908 [g-32P]-ATP MP Biochemicals Cat# 0135001 [8-14C]-ADP Perkin Elmer Cat# 0113004 D-[5-3H]-glucose Perkin Elmer Cat# NET53100 13C6-glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396 13C5-glutamine Cambridge Isotope Laboratories, Inc. Cat# CLM-1822 LY294002 Selleck Chemicals Cat# S1105 MK-2206 Selleck Chemicals Cat# S1078 Critical Commercial Assays ATP Colorimetric/Fluorometric Assay Kit BioVision Cat# K354-100 L-Lactate Assay Kit II Eton Bioscience Cat# 120005 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 Tumor Dissociation Kit, mouse Miltenyi Biotec Inc. Cat# 130-096-730 VECTASTAIN Elite ABC HRP Kit Vector Laboratories Cat# PK-6101 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 Seahorse XF Analyzer Agilent Technologies N/A Malachite Green Assay Kit Echelon Biosciences Inc Cat# K-1500 SensoLyte FDP Protein Phosphatase Assay Kit AnaSpec Co Cat# AS-71100 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Deposited Data Raw Data This paper, Mendeley Data https://data.mendeley.com/datasets/ 3s8ny9vh85/draft?a=2b486ba9-a27745a6-bfb7-546f806deb7a Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: A172 ATCC Cat# CRL-1620 Human: LN229 ATCC Cat# CRL-2611 Human: LN18 ATCC Cat# CRL-2610 Human: HEK293T ATCC Cat# CRL-11268 Mouse: Pten+/+ MEFs Wang et al., 2011 N/A Mouse: Pten / MEFs Wang et al., 2011 N/A Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas N/A MD Anderson Cancer Center Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides PGK1 pY324 peptide (318-PESSKK-pY-AEAVTR-330) This paper, synthesized by Selleck Chemicals N/A acidic standard PTEN substrate peptide poly-(EY) (RRREEEpYEEE) This paper, synthesized by Selleck Chemicals N/A Primers used in this paper, see Table S3 This paper N/A (Continued on next page) e2 Molecular Cell 76, 1–12.e1–e7, November 7, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
TUNEL Assay:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER HA peptide ThermoFisher Scientific Cat# 26184 Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-DYKDDDDK Tag (L5) Affinity Gel BioLegend Cat# 651503 Anti-c-Myc Tag (9E10) Affinity Gel BioLegend Cat# 658502 Ni-NTA His,Bind Resin EMD Millipore Cat# 70666 Phosphatidylinositol 3,4,5-trisphosphate diC8 (diC8-PI [3,4,5]P3) Echelon Biosciences, Inc. Cat# P-3908 [g-32P]-ATP MP Biochemicals Cat# 0135001 [8-14C]-ADP Perkin Elmer Cat# 0113004 D-[5-3H]-glucose Perkin Elmer Cat# NET53100 13C6-glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396 13C5-glutamine Cambridge Isotope Laboratories, Inc. Cat# CLM-1822 LY294002 Selleck Chemicals Cat# S1105 MK-2206 Selleck Chemicals Cat# S1078 Critical Commercial Assays ATP Colorimetric/Fluorometric Assay Kit BioVision Cat# K354-100 L-Lactate Assay Kit II Eton Bioscience Cat# 120005 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 Tumor Dissociation Kit, mouse Miltenyi Biotec Inc. Cat# 130-096-730 VECTASTAIN Elite ABC HRP Kit Vector Laboratories Cat# PK-6101 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 Seahorse XF Analyzer Agilent Technologies N/A Malachite Green Assay Kit Echelon Biosciences Inc Cat# K-1500 SensoLyte FDP Protein Phosphatase Assay Kit AnaSpec Co Cat# AS-71100 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Deposited Data Raw Data This paper, Mendeley Data https://data.mendeley.com/datasets/ 3s8ny9vh85/draft?a=2b486ba9-a27745a6-bfb7-546f806deb7a Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: A172 ATCC Cat# CRL-1620 Human: LN229 ATCC Cat# CRL-2611 Human: LN18 ATCC Cat# CRL-2610 Human: HEK293T ATCC Cat# CRL-11268 Mouse: Pten+/+ MEFs Wang et al., 2011 N/A Mouse: Pten / MEFs Wang et al., 2011 N/A Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas N/A MD Anderson Cancer Center Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides PGK1 pY324 peptide (318-PESSKK-pY-AEAVTR-330) This paper, synthesized by Selleck Chemicals N/A acidic standard PTEN substrate peptide poly-(EY) (RRREEEpYEEE) This paper, synthesized by Selleck Chemicals N/A Primers used in this paper, see Table S3 This paper N/A (Continued on next page) e2 Molecular Cell 76, 1–12.e1–e7, November 7, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Synthesized:Article Title: PTEN Suppresses Glycolysis by Dephosphorylating and Inhibiting Autophosphorylated PGK1.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER HA peptide ThermoFisher Scientific Cat# 26184 Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-DYKDDDDK Tag (L5) Affinity Gel BioLegend Cat# 651503 Anti-c-Myc Tag (9E10) Affinity Gel BioLegend Cat# 658502 Ni-NTA His,Bind Resin EMD Millipore Cat# 70666 Phosphatidylinositol 3,4,5-trisphosphate diC8 (diC8-PI [3,4,5]P3) Echelon Biosciences, Inc. Cat# P-3908 [g-32P]-ATP MP Biochemicals Cat# 0135001 [8-14C]-ADP Perkin Elmer Cat# 0113004 D-[5-3H]-glucose Perkin Elmer Cat# NET53100 13C6-glucose Cambridge Isotope Laboratories, Inc. Cat# CLM-1396 13C5-glutamine Cambridge Isotope Laboratories, Inc. Cat# CLM-1822 LY294002 Selleck Chemicals Cat# S1105 MK-2206 Selleck Chemicals Cat# S1078 Critical Commercial Assays ATP Colorimetric/Fluorometric Assay Kit BioVision Cat# K354-100 L-Lactate Assay Kit II Eton Bioscience Cat# 120005 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 Tumor Dissociation Kit, mouse Miltenyi Biotec Inc. Cat# 130-096-730 VECTASTAIN Elite ABC HRP Kit Vector Laboratories Cat# PK-6101 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 Seahorse XF Analyzer Agilent Technologies N/A Malachite Green Assay Kit Echelon Biosciences Inc Cat# K-1500 SensoLyte FDP Protein Phosphatase Assay Kit AnaSpec Co Cat# AS-71100 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Deposited Data Raw Data This paper, Mendeley Data https://data.mendeley.com/datasets/ 3s8ny9vh85/draft?a=2b486ba9-a27745a6-bfb7-546f806deb7a Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: A172 ATCC Cat# CRL-1620 Human: LN229 ATCC Cat# CRL-2611 Human: LN18 ATCC Cat# CRL-2610 Human: HEK293T ATCC Cat# CRL-11268 Mouse: Pten+/+ MEFs Wang et al., 2011 N/A Mouse: Pten / MEFs Wang et al., 2011 N/A Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas N/A MD Anderson Cancer Center Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides PGK1 pY324 peptide (318-PESSKK-pY-AEAVTR-330) This paper, synthesized by Selleck Chemicals N/A acidic standard PTEN substrate peptide poly-(EY) (RRREEEpYEEE) This paper, synthesized by Selleck Chemicals N/A Primers used in this paper, see Table S3 This paper N/A (Continued on next page) e2 Molecular Cell 76, 1–12.e1–e7, November 7, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pGIPZ PTEN shRNA Dharmacon V2LHS_92314 pcDNA3.1 HA-PTEN WT This paper N/A pcDNA3.1 HA-PTEN C124S This paper N/A pcDNA3.1 HA-PTEN G129E This paper N/A pcDNA3.1 HA-PTEN Y138L This paper N/A pcDNA3.1 Flag-PTEN WT This paper N/A pcDNA3.1 Flag-PTEN C124S This paper N/A pcDNA3.1 Flag-PTEN D92A This paper N/A pColdI PTEN WT This paper N/A pColdI PTEN C124S This paper N/A pColdI PTEN G129E This paper N/A pColdI PTEN Y138L This paper N/A pGIPZ PGK1 shRNA Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 WT Qian et al., 2017a N/A pcDNA3.1 HA-PGK1 T378P This paper N/A pcDNA3.1 Flag-PGK1 WT This paper N/A pcDNA3.1 Flag-PGK1 Y324F This paper N/A pcDNA3.1 Flag-PGK1 S203A This paper N/A pcDNA3.1 Flag-PGK1 S256A This paper N/A pcDNA6-SFB PGK1 WT This paper N/A pcDNA6-SFB PGK1 Y324F This paper N/A pcDNA6-SFB PGK1 T378P This paper N/A PGEX-4T-1 PGK1 WT This paper N/A PGEX-4T-1 PGK1 T378P This paper N/A PGEX-4T-1 PGK1 Y324F/T378P This paper N/A pColdI PGK1 WT This paper N/A pColdI PGK1 Y324F This paper N/A pColdI PGK1 T378P This paper N/A pcDNA3.1 Flag-Beclin1 WT Qian et al., 2017a N/A pcDNA3.1 Flag-Beclin1 S30A Qian et al., 2017a N/A PX458 Ran et al., 2013 Addgene #48138 HA-Myr-AKT Addgene Cat# 10841 Flag-PTP-PEST Zheng et al., 2009 N/A HA-RPTPa Zheng et al., 2009 N/A Myc-SHP1 Zheng et al., 2009 N/A Myc-SHP2 Zheng et al., 2009 N/A Software and Algorithms Protein Data Bank RCSB PDB www.rcsb.org Discover Studio Visualizer Accelrys accelrys.com UCSF Chimera UCSF www.cgl.ucsf.edu/chimera Amber 16 Molecular Dynamics package UCSF ambermd.org PyMOL Schrödinger, LLC https://pymol.org/2/ SeeSAR BioSolveIT GmbH https://www.biosolveit.de/SeeSAR CRISPR Design tool Zhang Lab https://zlab.bio/guide-design-resources Molecular Cell 76, 1–12.e1–e7, November 7, 2019 e3
Virus:Article Title: Small-molecule inhibitors of the protein kinase DYRK as potential therapeutic candidates in cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYRK1A Santa Cruz Cat# sc-100376; RRID: AB_1122375 EGFR Santa Cruz Cat# sc-373746; RRID: AB_10920395 GAPDH Santa Cruz Cat# sc-47724; RRID: AB_627678 pERK Cell Signaling Cat# 9101; RRID: AB_331646 ERK Santa Cruz Cat# sc-514302; RRID: AB_2571739 HA antibody GenScript Cat# A01621; RRID: AB_2622159 c-Cbl Cell Signaling Cat# 2747; RRID: AB_2275284 DYRK2 Santa Cruz Cat# sc-293487 DYRK3 Santa Cruz Cat# sc-390532 HRP goat anti-mouse Abcam Cat# ab6789; RRID: AB_955439 HRP goat anti-rabbit Abcam Cat# ab6721; RRID: AB_955447 Sprouty2 Santa Cruz Cat# sc-518014 Bacterial and virus strains One ShotTM BL21(DE3) Chemically Competent E. coli Thermo Fisher Cat# C600003 Rosetta (DE3) Competent Cells - Novagen Millipore Sigma Cat# 70954-3 One ShotTM Stbl3TM Chemically Competent E. coli Thermo Fisher Cat# C737303 Chemicals, peptides, and recombinant proteins MG132 Sigma Cat# M8699 Bafilomycin A1 (BaFA1) Tocris Bioscience Cat# 1334 B-27 Supplement minus Vitamin-A Invitrogen Cat# 12587010 Human EGF Fujifilm Biosciences Cat# 100-26 Human FGF-2 Fujifilm Biosciences Cat# 100-28 Human PGDF-AA Fujifilm Biosciences Cat# 100-16 Human PGDF-BB Fujifilm Biosciences Cat# 100-18 Heparin StemCell Technologies Cat# 07980 Critical commercial assays ADP-Glo Kinase assay kit Promega Cat# V6930 PierceTM BCA Protein Assay kit Thermo Fisher Cat# 23225 Quik Change II Site-directed Mutagenesis kit Agilent technologies Cat# 200523 Deposited data DYRK1A – FC-3 crystal structure This paper PDB ID: 9YKO https://www.rcsb.org/ structure/9YKO Experimental models: Cell lines Human: U87MG cells ATCC Cat# HTB-14 Human: LN229 cells ATCC Cat# CRL-2611 (Continued on next page) ll OPEN ACCESS Article e1 Cell Chemical Biology 33, 1–13.e1–e7, June 18, 2026 ..
Recombinant:Article Title: Small-molecule inhibitors of the protein kinase DYRK as potential therapeutic candidates in cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYRK1A Santa Cruz Cat# sc-100376; RRID: AB_1122375 EGFR Santa Cruz Cat# sc-373746; RRID: AB_10920395 GAPDH Santa Cruz Cat# sc-47724; RRID: AB_627678 pERK Cell Signaling Cat# 9101; RRID: AB_331646 ERK Santa Cruz Cat# sc-514302; RRID: AB_2571739 HA antibody GenScript Cat# A01621; RRID: AB_2622159 c-Cbl Cell Signaling Cat# 2747; RRID: AB_2275284 DYRK2 Santa Cruz Cat# sc-293487 DYRK3 Santa Cruz Cat# sc-390532 HRP goat anti-mouse Abcam Cat# ab6789; RRID: AB_955439 HRP goat anti-rabbit Abcam Cat# ab6721; RRID: AB_955447 Sprouty2 Santa Cruz Cat# sc-518014 Bacterial and virus strains One ShotTM BL21(DE3) Chemically Competent E. coli Thermo Fisher Cat# C600003 Rosetta (DE3) Competent Cells - Novagen Millipore Sigma Cat# 70954-3 One ShotTM Stbl3TM Chemically Competent E. coli Thermo Fisher Cat# C737303 Chemicals, peptides, and recombinant proteins MG132 Sigma Cat# M8699 Bafilomycin A1 (BaFA1) Tocris Bioscience Cat# 1334 B-27 Supplement minus Vitamin-A Invitrogen Cat# 12587010 Human EGF Fujifilm Biosciences Cat# 100-26 Human FGF-2 Fujifilm Biosciences Cat# 100-28 Human PGDF-AA Fujifilm Biosciences Cat# 100-16 Human PGDF-BB Fujifilm Biosciences Cat# 100-18 Heparin StemCell Technologies Cat# 07980 Critical commercial assays ADP-Glo Kinase assay kit Promega Cat# V6930 PierceTM BCA Protein Assay kit Thermo Fisher Cat# 23225 Quik Change II Site-directed Mutagenesis kit Agilent technologies Cat# 200523 Deposited data DYRK1A – FC-3 crystal structure This paper PDB ID: 9YKO https://www.rcsb.org/ structure/9YKO Experimental models: Cell lines Human: U87MG cells ATCC Cat# HTB-14 Human: LN229 cells ATCC Cat# CRL-2611 (Continued on next page) ll OPEN ACCESS Article e1 Cell Chemical Biology 33, 1–13.e1–e7, June 18, 2026 ..
Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Kinase Assay:Article Title: Small-molecule inhibitors of the protein kinase DYRK as potential therapeutic candidates in cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYRK1A Santa Cruz Cat# sc-100376; RRID: AB_1122375 EGFR Santa Cruz Cat# sc-373746; RRID: AB_10920395 GAPDH Santa Cruz Cat# sc-47724; RRID: AB_627678 pERK Cell Signaling Cat# 9101; RRID: AB_331646 ERK Santa Cruz Cat# sc-514302; RRID: AB_2571739 HA antibody GenScript Cat# A01621; RRID: AB_2622159 c-Cbl Cell Signaling Cat# 2747; RRID: AB_2275284 DYRK2 Santa Cruz Cat# sc-293487 DYRK3 Santa Cruz Cat# sc-390532 HRP goat anti-mouse Abcam Cat# ab6789; RRID: AB_955439 HRP goat anti-rabbit Abcam Cat# ab6721; RRID: AB_955447 Sprouty2 Santa Cruz Cat# sc-518014 Bacterial and virus strains One ShotTM BL21(DE3) Chemically Competent E. coli Thermo Fisher Cat# C600003 Rosetta (DE3) Competent Cells - Novagen Millipore Sigma Cat# 70954-3 One ShotTM Stbl3TM Chemically Competent E. coli Thermo Fisher Cat# C737303 Chemicals, peptides, and recombinant proteins MG132 Sigma Cat# M8699 Bafilomycin A1 (BaFA1) Tocris Bioscience Cat# 1334 B-27 Supplement minus Vitamin-A Invitrogen Cat# 12587010 Human EGF Fujifilm Biosciences Cat# 100-26 Human FGF-2 Fujifilm Biosciences Cat# 100-28 Human PGDF-AA Fujifilm Biosciences Cat# 100-16 Human PGDF-BB Fujifilm Biosciences Cat# 100-18 Heparin StemCell Technologies Cat# 07980 Critical commercial assays ADP-Glo Kinase assay kit Promega Cat# V6930 PierceTM BCA Protein Assay kit Thermo Fisher Cat# 23225 Quik Change II Site-directed Mutagenesis kit Agilent technologies Cat# 200523 Deposited data DYRK1A – FC-3 crystal structure This paper PDB ID: 9YKO https://www.rcsb.org/ structure/9YKO Experimental models: Cell lines Human: U87MG cells ATCC Cat# HTB-14 Human: LN229 cells ATCC Cat# CRL-2611 (Continued on next page) ll OPEN ACCESS Article e1 Cell Chemical Biology 33, 1–13.e1–e7, June 18, 2026 ..
Bicinchoninic Acid Protein Assay:Article Title: Small-molecule inhibitors of the protein kinase DYRK as potential therapeutic candidates in cancer.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies DYRK1A Santa Cruz Cat# sc-100376; RRID: AB_1122375 EGFR Santa Cruz Cat# sc-373746; RRID: AB_10920395 GAPDH Santa Cruz Cat# sc-47724; RRID: AB_627678 pERK Cell Signaling Cat# 9101; RRID: AB_331646 ERK Santa Cruz Cat# sc-514302; RRID: AB_2571739 HA antibody GenScript Cat# A01621; RRID: AB_2622159 c-Cbl Cell Signaling Cat# 2747; RRID: AB_2275284 DYRK2 Santa Cruz Cat# sc-293487 DYRK3 Santa Cruz Cat# sc-390532 HRP goat anti-mouse Abcam Cat# ab6789; RRID: AB_955439 HRP goat anti-rabbit Abcam Cat# ab6721; RRID: AB_955447 Sprouty2 Santa Cruz Cat# sc-518014 Bacterial and virus strains One ShotTM BL21(DE3) Chemically Competent E. coli Thermo Fisher Cat# C600003 Rosetta (DE3) Competent Cells - Novagen Millipore Sigma Cat# 70954-3 One ShotTM Stbl3TM Chemically Competent E. coli Thermo Fisher Cat# C737303 Chemicals, peptides, and recombinant proteins MG132 Sigma Cat# M8699 Bafilomycin A1 (BaFA1) Tocris Bioscience Cat# 1334 B-27 Supplement minus Vitamin-A Invitrogen Cat# 12587010 Human EGF Fujifilm Biosciences Cat# 100-26 Human FGF-2 Fujifilm Biosciences Cat# 100-28 Human PGDF-AA Fujifilm Biosciences Cat# 100-16 Human PGDF-BB Fujifilm Biosciences Cat# 100-18 Heparin StemCell Technologies Cat# 07980 Critical commercial assays ADP-Glo Kinase assay kit Promega Cat# V6930 PierceTM BCA Protein Assay kit Thermo Fisher Cat# 23225 Quik Change II Site-directed Mutagenesis kit Agilent technologies Cat# 200523 Deposited data DYRK1A – FC-3 crystal structure This paper PDB ID: 9YKO https://www.rcsb.org/ structure/9YKO Experimental models: Cell lines Human: U87MG cells ATCC Cat# HTB-14 Human: LN229 cells ATCC Cat# CRL-2611 (Continued on next page) ll OPEN ACCESS Article e1 Cell Chemical Biology 33, 1–13.e1–e7, June 18, 2026 ..
SYBR Green Assay:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Chromatin Immunoprecipitation:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
ROS Assay:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Reporter Assay:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
shRNA:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Sequencing:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
Pyrolysis Gas Chromatography:Article Title: KDM3A Senses Oxygen Availability to Regulate PGC-1α-Mediated Mitochondrial Biogenesis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER iQ SYBR Green Supermix Bio-Rad Cat# 170-8882 SimpleChIP plus Enzymatic Chromatin IP kit Cell Signaling Technology Cat# 9003 MitoTracker Red CMXRos ThermoFisher Scientific Cat# M7512 VECTASTAIN ABC kit Vector Laboratories Cat# PK-4000 Liquid DAB+ Substrate Chromogen System Dako Cat# K3468 QuikChange site-directed mutagenesis kit Agilent Technologies Cat# 200524 DCFDA / H2DCFDA - Cellular ROS Assay Kit Abcam Cat# ab113851 DeadEnd Colorimetric TUNEL System Promega Cat# G7360 Dual-Luciferase Reporter Assay System Promega Cat# E1910 Deposited Data Raw Data This paper, Mendeley Data https://doi.org/10.17632/wk3myh726s.1 Experimental Models: Cell Lines Human: U87 ATCC Cat# HTB-14 Human: U251 Sigma-Aldrich Cat# 09063001 Human: T98G ATCC Cat# CRL-1690 Human: NHA Lonza Cat# CC-2565 Human: MD-MB-231 ATCC Cat# HTB-26 Human: BxPC-3 ATCC Cat# CRL-1687 Human: HeLa ATCC Cat# CCL-2 Human: HepG2 ATCC Cat# HB-8065 Human: 293T ATCC Cat# CRL-11268 Experimental Models: Organisms/Strains Mouse: BALB/c nude The University of Texas MD Anderson Cancer Center N/A Mouse: BALB/c nude Model Animal Research Center of Nanjing University N/A Oligonucleotides shRNA sequence targeting PGC-1a: TTACCGACATAAATCACAC N/A N/A shRNA sequence targeting KDM3A #1: TGATCATGAATAGGATCGT This paper N/A shRNA sequence targeting KDM3A #2: TTCCTGAACAGTTATTAGG This paper N/A shRNA sequence targeting HIF-1a: TTCATATCCAGGCTGTGTC This paper N/A Primers used in this paper, see Table S1 This paper N/A Recombinant DNA Flag-PGC-1a This paper N/A Flag-PGC-1a K224R This paper N/A Flag-rPGC-1a This paper N/A Flag-rPGC-1a K224R This paper N/A Flag-PGC-1a 1-403 This paper N/A Flag-PGC-1a 404-798 This paper N/A Flag-PGC-1a DRRM This paper N/A Flag-PGC-1a DSR This paper N/A Flag-KDM3A This paper N/A Flag-KDM3A H1120Y This paper N/A Flag-rKDM3A This paper N/A Flag-rKDM3A H1120Y This paper N/A (Continued on next page) Molecular Cell 76, 1–11.e1–e7, December 19, 2019 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER HA-KDM3A This paper N/A HA-KDM3A H1120Y This paper N/A Flag-KDM1A This paper N/A Flag-KDM2A Wagner et al., 2013 N/A Flag-Kdm2b He et al., 2013 Addgene# 61739 Flag-KDM4A This paper N/A Flag-KDM4B This paper N/A Flag-KDM4C This paper N/A Flag-Kdm4d Matoba et al., 2014 Addgene# 61553 Flag-Kdm5b This paper N/A Flag-KDM5C This paper N/A Flag-KDM5D Li et al., 2016a N/A Flag-KDM6A This paper N/A Flag-KDM6B This paper N/A Flag-KDM6C This paper N/A Flag-KDM7A Osawa et al., 2011 N/A Flag-KDM7C This paper N/A Flag-KDM8 This paper N/A Flag-HR Liu et al., 2014 N/A HA-ERRa This paper N/A HA-PPARa This paper N/A HA-YY1 This paper N/A HA-NRF1 This paper N/A HA-HCF1 Wilson et al., 1993 Addgene# 53309 PX458 (pSpCas9(BB)-2A-GFP) Ran et al., 2013 Addgene# 48138 pGL3-TFAM/NRF1-Luc This paper N/A pGL3-TFAM/NRF2a-Luc This paper N/A pGL3-TFB1M( 201)-Luc This paper N/A pGL3-TFB2M( 80)-Luc This paper N/A Software and Algorithms ImageJ NIH N/A CRISPR Design tool Zhang Lab http://zlab.bio/guide-design-resources
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