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Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol 2012; 13:418. [PMID: 22889292 PMCID: PMC3491367 DOI: 10.1186/gb-2012-13-8-418] [Citation(s) in RCA: 343] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.
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Affiliation(s)
- John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ross Hardison
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Thomas Gingeras
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Mark Groudine
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael Bender
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rajinder Kaul
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Theresa Canfield
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Erica Giste
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Audra Johnson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mia Zhang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gayathri Balasundaram
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rachel Byron
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Vaughan Roach
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Peter J Sabo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Richard Sandstrom
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - A Sandra Stehling
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Robert E Thurman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Philip Cayting
- Department of Genetics, Yale University, New Haven, Connecticut, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Manoj Hariharan
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Lian
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Yong Cheng
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen G Landt
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Barbara J Wold
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA
| | - Gregory E Crawford
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Cheryl A Keller
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Weisheng Wu
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christopher Morrissey
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Swathi A Kumar
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tejaswini Mishra
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Deepti Jain
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Marta Byrska-Bishop
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Daniel Blankenberg
- Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bryan R Lajoie1
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Gaurav Jain
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA
| | - Amartya Sanyal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA
| | - Kaun-Bei Chen
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
| | - Olgert Denas
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
| | - James Taylor
- Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA
| | - Gerd A Blobel
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Mitchell J Weiss
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Max Pimkin
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Wulan Deng
- Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA
| | - Georgi K Marinov
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Brian A Williams
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | | | - Gilberto Desalvo
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Anthony Kiralusha
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Diane Trout
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Henry Amrhein
- Div. of Biology, California Institute of Technology, Pasadena, California, USA
| | - Ali Mortazavi
- Dept. of Developmental and Cell Biology, University of California Irvine, Irvine California, USA
| | - Lee Edsall
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - David McCleary
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Samantha Kuan
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Yin Shen
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Feng Yue
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Zhen Ye
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - Carrie A Davis
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Chris Zaleski
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sonali Jha
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Chenghai Xue
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Alex Dobin
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Wei Lin
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Meagan Fastuca
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Huaien Wang
- Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Roderic Guigo
- Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain
| | - Sarah Djebali
- Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain
| | - Julien Lagarde
- Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain
| | - Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Venkat S Malladi
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Melissa S Cline
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Vanessa M Kirkup
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Katrina Learned
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Kate R Rosenbloom
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - W James Kent
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
| | - Elise A Feingold
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter J Good
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Pazin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebecca F Lowdon
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Leslie B Adams
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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