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An encyclopedia of mouse DNA elements (Mouse ENCODE)

Mouse ENCODE Consortium, John A Stamatoyannopoulos1*, Michael Snyder2, Ross Hardison3, Bing Ren4, Thomas Gingeras5, David M Gilbert6, Mark Groudine7, Michael Bender7, Rajinder Kaul1, Theresa Canfield1, Erica Giste1, Audra Johnson1, Mia Zhang7, Gayathri Balasundaram7, Rachel Byron7, Vaughan Roach1, Peter J Sabo1, Richard Sandstrom1, A Sandra Stehling1, Robert E Thurman1, Sherman M Weissman8, Philip Cayting1089, Manoj Hariharan2, Jin Lian9, Yong Cheng2, Stephen G Landt2, Zhihai Ma2, Barbara J Wold11, Job Dekker12, Gregory E Crawford1314, Cheryl A Keller3, Weisheng Wu3, Christopher Morrissey3, Swathi A Kumar3, Tejaswini Mishra3, Deepti Jain3, Marta Byrska-Bishop3, Daniel Blankenberg3, Bryan R Lajoie12, Gaurav Jain12, Amartya Sanyal12, Kaun-Bei Chen13, Olgert Denas13, James Taylor15, Gerd A Blobel16, Mitchell J Weiss16, Max Pimkin16, Wulan Deng16, Georgi K Marinov11, Brian A Williams11, Katherine I Fisher-Aylor11, Gilberto Desalvo11, Anthony Kiralusha11, Diane Trout11, Henry Amrhein11, Ali Mortazavi17, Lee Edsall4, David McCleary4, Samantha Kuan4, Yin Shen4, Feng Yue4, Zhen Ye4, Carrie A Davis5, Chris Zaleski5, Sonali Jha5, Chenghai Xue5, Alex Dobin5, Wei Lin5, Meagan Fastuca5, Huaien Wang5, Roderic Guigo18, Sarah Djebali18, Julien Lagarde18, Tyrone Ryba6, Takayo Sasaki6, Venkat S Malladi19, Melissa S Cline19, Vanessa M Kirkup19, Katrina Learned19, Kate R Rosenbloom19, W James Kent19, Elise A Feingold20, Peter J Good20, Michael Pazin20, Rebecca F Lowdon20 and Leslie B Adams20

  • * Corresponding author: John A Stamatoyannopoulos jstam@uw.edu

Author Affiliations

1 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA

2 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA

3 Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA

4 Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California San Diego, La Jolla, California, USA

5 Dept. of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

6 Department of Biological Science, Florida State University, Tallahassee, Florida, USA

7 Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

8 Department of Genetics, Yale University, New Haven, Connecticut, USA

9 Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA

10 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA

11 Div. of Biology, California Institute of Technology, Pasadena, California, USA

12 Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachussetts, USA

13 Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA

14 Department of Pediatrics, Duke University, Durham, North Carolina, USA

15 Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA

16 Div. of Hematology, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, Pennsylvania, USA

17 Dept. of Developmental and Cell Biology, University of California Irvine, Irvine California, USA

18 Division of Bioinformatics and Genomics, Center for Genomic Regulation, Barcelona, Catalunya, Spain

19 Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, California, USA

20 National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA

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Genome Biology 2012, 13:418  doi:10.1186/gb-2012-13-8-418

Published: 13 August 2012

Additional files

Additional file 1:

Table S1 - overview of Mouse ENCODE data. Snapshot of data generated by the Mouse ENCODE Consortium and released through University of California Santa Cruz (UCSC) browser. Vertical axis: cell lines and ex vivo cells and tissues. The originating cell type is shown in parentheses next to each line. For mouse embryonic or fetal tissues, the developmental day of harvest is shown in parentheses. Unless otherwise noted, all other tissues are from adult animals. Horizontal axis: experimental assays, including DNaseI hypersensitivity sites (DNaseI), DNaseI footprints by digital genomic footprinting (DGF); mRNA-seq; DNA replication type by Repli-chIP; modifications to histone H3, including bulk acetylation (H3ac) or modification to specific lysine positions on the H3 tail; ChIP-seq for polymerase (Pol2, Pol2-4H8), histone acetyltransferase p300, and diverse transcrition factors; and ChIP input control (far right lane). Filled cells indicate that an assay has been performed by the indicated production center(s) and data released to UCSC.

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