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Kaloff C, Anastassiadis K, Ayadi A, Baldock R, Beig J, Birling MC, Bradley A, Brown S, Bürger A, Bushell W, Chiani F, Collins FS, Doe B, Eppig JT, Finnel RH, Fletcher C, Flicek P, Fray M, Friedel RH, Gambadoro A, Gates H, Hansen J, Herault Y, Hicks GG, Hörlein A, Hrabé de Angelis M, Iyer V, de Jong PJ, Koscielny G, Kühn R, Liu P, Lloyd KC, Lopez RG, Marschall S, Martínez S, McKerlie C, Meehan T, von Melchner H, Moore M, Murray SA, Nagy A, Nutter L, Pavlovic G, Pombero A, Prosser H, Ramirez-Solis R, Ringwald M, Rosen B, Rosenthal N, Rossant J, Ruiz Noppinger P, Ryder E, Skarnes WC, Schick J, Schnütgen F, Schofield P, Seisenberger C, Selloum M, Smedley D, Simpson EM, Stewart AF, Teboul L, Tocchini Valentini GP, Valenzuela D, West A, Wurst W. Genome Wide Conditional Mouse Knockout Resources. DRUG DISCOVERY TODAY. DISEASE MODELS 2017; 20:3-12. [PMID: 39132094 PMCID: PMC11315453 DOI: 10.1016/j.ddmod.2017.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The International Knockout Mouse Consortium (IKMC) developed high throughput gene trapping and gene targeting pipelines that produced mostly conditional mutations of more than 18,500 genes in C57BL/6N mouse embryonic stem (ES) cells which have been archived and are freely available to the research community as a frozen resource. From this unprecedented resource more than 6,000 mutant mouse strains have been produced by the IKMC and mostly the International Mouse Phenotyping Consortium (IMPC). In addition, a cre-driver resource was established including 250 inducible cre-driver mouse strains in a C57BL/6 background. Complementing the cre-driver resource, a collection of comprising 27 cre-driver rAAVs has also been produced. The resources can be easily accessed at the IKMC/IMPC web portal (www.mousephenotype.org). The IKMC/IMPC resource is a standardized reference library of mouse models with defined genetic backgrounds that enables the analysis of gene-disease associations in mice of different genetic makeup and should therefore have a major impact on biomedical research.
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Affiliation(s)
- C Kaloff
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - K Anastassiadis
- Biotechnology Center (BIOTEC) of the Technische Universität Dresden, 01307 Dresden, Germany
| | - A Ayadi
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
| | - R Baldock
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, College of Medicine and Veterinary Medicine, Edinburgh, Scotland EH4 2XU, UK
| | - J Beig
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - M-C Birling
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
| | - A Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - S Brown
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX110RD, UK
| | - A Bürger
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - W Bushell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - F Chiani
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, I-00015 Rome, Italy
| | - F S Collins
- Office of the Director, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - B Doe
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - J T Eppig
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - R H Finnel
- The Texas A&M Institute for Genomic Medicine, College Station, Texas, 77843-4485 USA; University of Texas at Austin, Austin, Texas, 78712, USA
| | - C Fletcher
- National Institutes of Health, Bethesda, Maryland, 20205, USA
| | - P Flicek
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB101ST, UK
| | - M Fray
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX110RD, UK
| | - R H Friedel
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - A Gambadoro
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, I-00015 Rome, Italy
| | - H Gates
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX110RD, UK
| | - J Hansen
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - Y Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - G G Hicks
- University of Manitoba, Manitoba Institute of Cell Biology, Winnipeg, MB, R3EOV9, Canada
| | - A Hörlein
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - M Hrabé de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - V Iyer
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - P J de Jong
- Children's Hospital Oakland Research Institute, CHORI, Oakland, CA, 94609, USA
| | - G Koscielny
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB101ST, UK
| | - R Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - P Liu
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - K C Lloyd
- Mouse Biology Program, School of Veterinary Medicine, University of California, Davis, California 95616, USA
| | - R G Lopez
- Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante
| | - S Marschall
- Institute of Experimental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - S Martínez
- Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante
| | - C McKerlie
- The Centre for Phenogenomics and Translation Medicine, The Hospital for Sick Children, Toronto, CANADA
| | - T Meehan
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB101ST, UK
| | - H von Melchner
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - M Moore
- IMPC, San Anselmo, California, US
| | - S A Murray
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - A Nagy
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON, M5G1X5, Canada
| | - Lmj Nutter
- The Centre for Phenogenomics and Translation Medicine, The Hospital for Sick Children, Toronto, CANADA
| | - G Pavlovic
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
| | - A Pombero
- Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante
| | - H Prosser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - R Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - M Ringwald
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - B Rosen
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - N Rosenthal
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - J Rossant
- Research Institute, The Hospital for Sick Children, SickKids Foundation, Toronto, ON, M5G2L3, Canada
| | - P Ruiz Noppinger
- Department of Vertebrate Genomics, Charité, 10115 Berlin, Germany
| | - E Ryder
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - W C Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - J Schick
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - F Schnütgen
- Department of Molecular Haematology, University of Frankfurt Medical School, 60590 Frankfurt am Main, Germany
| | - P Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB23EG, UK
| | - C Seisenberger
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
| | - M Selloum
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
| | - D Smedley
- European Bioinformatics Institute (EBI), Hinxton, Cambridge, CB101ST, UK
- Clinical Pharmacology, Queen Mary, University of London, Gower Street, London WC1E 6BT, UK
| | - E M Simpson
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - A F Stewart
- Biotechnology Center (BIOTEC) of the Technische Universität Dresden, 01307 Dresden, Germany
| | - L Teboul
- Mammalian Genetics Unit, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX110RD, UK
| | - G P Tocchini Valentini
- Istituto di Biologia Cellulare, Consiglio Nazionale delle Ricerche (CNR), Monterotondo-Scalo, I-00015 Rome, Italy
| | - D Valenzuela
- Velocigene Division, Regeneron Pharmaceuticals Inc., Tarrytown, New York, 10591, USA
| | - A West
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101HH, UK
| | - W Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, D-85764 Neuherberg, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München - Feodor-Lynen-Str. 17, 81377 München Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377 Munich, Germany
- Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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Zhang B, Chen B, Wu T, Tan Y, Qiu S, Xuan Z, Zhu X, Chen R. Estimating the quality of reprogrammed cells using ES cell differentiation expression patterns. PLoS One 2011; 6:e15336. [PMID: 21283513 PMCID: PMC3023460 DOI: 10.1371/journal.pone.0015336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Accepted: 11/07/2010] [Indexed: 02/02/2023] Open
Abstract
Somatic cells can be reprogrammed to a pluripotent state by over-expression of defined factors, and pluripotency has been confirmed by the tetraploid complementation assay. However, especially in human cells, estimating the quality of Induced Pluripotent Stem Cell(iPSC) is still difficult. Here, we present a novel supervised method for the assessment of the quality of iPSCs by estimating the gene expression profile using a 2-D “Differentiation-index coordinate”, which consists of two “developing lines” that reflects the directions of ES cell differentiation and the changes of cell states during differentiation. By applying a novel liner model to describe the differentiation trajectory, we transformed the ES cell differentiation time-course expression profiles to linear “developing lines”; and use these lines to construct the 2-D “Differentiation-index coordinate” of mouse and human. We compared the published gene expression profiles of iPSCs, ESCs and fibroblasts in mouse and human “Differentiation-index coordinate”. Moreover, we defined the Distance index to indicate the qualities of iPS cells, which based on the projection distance of iPSCs-ESCs and iPSCs-fibroblasts. The results indicated that the “Differentiation-index coordinate” can distinguish differentiation states of the different cells types. Furthermore, by applying this method to the analysis of expression profiles in the tetraploid complementation assay, we showed that the Distance index which reflected spatial distributions correlated the pluripotency of iPSCs. We also analyzed the significantly changed gene sets of “developing lines”. The results suggest that the method presented here is not only suitable for the estimation of the quality of iPS cells based on expression profiles, but also is a new approach to analyze time-resolved experimental data.
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Affiliation(s)
- Bo Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Beibei Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tao Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yuliang Tan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shuang Qiu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenyu Xuan
- Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America
| | - Xiaopeng Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (XZ); (RC)
| | - Runsheng Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (XZ); (RC)
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Tsakiridis A, Tzouanacou E, Rahman A, Colby D, Axton R, Chambers I, Wilson V, Forrester L, Brickman JM. Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells. Nucleic Acids Res 2009; 37:e129. [PMID: 19692586 PMCID: PMC2770648 DOI: 10.1093/nar/gkp640] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/13/2009] [Accepted: 07/17/2009] [Indexed: 12/04/2022] Open
Abstract
Promoterless gene trap vectors have been widely used for high-efficiency gene targeting and random mutagenesis in embryonic stem (ES) cells. Unfortunately, such vectors are only effective for genes expressed in ES cells and this has prompted the development of expression-independent vectors. These polyadenylation (poly A) trap vectors employ a splice donor to capture an endogenous gene's polyadenylation sequence and provide transcript stability. However, the spectrum of mutations generated by these vectors appears largely restricted to the last intron of target loci due to nonsense-mediated mRNA decay (NMD) making them unsuitable for gene targeting applications. Here, we present novel poly A trap vectors that overcome the effect of NMD and also employ RNA instability sequences to improve splicing efficiency. The set of random insertions generated with these vectors show a significantly reduced insertional bias and the vectors can be targeted directly to a 5' intron. We also show that this relative positional independence is linked to the human beta-actin promoter and is most likely a result of its transcriptional activity in ES cells. Taken together our data indicate that these vectors are an effective tool for insertional mutagenesis that can be used for either gene trapping or gene targeting.
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Affiliation(s)
- Anestis Tsakiridis
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Elena Tzouanacou
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Afifah Rahman
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Richard Axton
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Lesley Forrester
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Joshua M. Brickman
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road and MRC Centre for Regenerative Medicine, Queens Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
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