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U.S.A."],"published-print":{"date-parts":[[2016,12,20]]},"abstract":"<jats:title>Significance<\/jats:title>\n                  <jats:p>Cloning cattle by somatic cell nuclear transfer (SCNT) is an agriculturally important technology and is also used as a model system for the study of mammalian development. The SCNT process is inefficient, typically yielding fewer than 10% live offspring. The majority of losses are the result of embryonic death, failure of the implantation process, and development of a defective placenta. A critical period is the implantation window, when survival of the conceptus depends on factors including genetics, epigenetics, and the communication between conceptus and the endometrium. Our study of gene expression in cloned conceptuses and endometrial tissues during the periimplantation period enhances understanding of the mechanisms that lead to pregnancy failure in SCNT cloning. The results have wide implications for cloning of other mammals.<\/jats:p>","DOI":"10.1073\/pnas.1520945114","type":"journal-article","created":{"date-parts":[[2016,12,8]],"date-time":"2016-12-08T22:45:33Z","timestamp":1481237133000},"page":"14492-14501","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":50,"title":["Massive dysregulation of genes involved in cell signaling and placental development in cloned cattle conceptus and maternal endometrium"],"prefix":"10.1073","volume":"113","author":[{"given":"Fernando H.","family":"Biase","sequence":"first","affiliation":[{"name":"Institute for Genomic Biology, University of Illinois at Urbana\u2013Champaign, Urbana, IL 61820;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanaka","family":"Rabel","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Illinois at Urbana\u2013Champaign, Urbana, IL 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Am J Reprod Immunol 58, 238\u2013254 (2007).","journal-title":"Am J Reprod Immunol"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","first-page":"230","DOI":"10.3389\/fimmu.2014.00230","article-title":"The role of placental tryptophan catabolism","volume":"5","author":"Sedlmayr P","year":"2014","unstructured":"P Sedlmayr, A Blaschitz, R Stocker, The role of placental tryptophan catabolism. Front Immunol 5, 230 (2014).","journal-title":"Front Immunol"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/0143-4004(92)90025-O","article-title":"Current topic: The synepitheliochorial placenta of ruminants: Binucleate cell fusions and hormone production","volume":"13","author":"Wooding FB","year":"1992","unstructured":"FB Wooding, Current topic: The synepitheliochorial placenta of ruminants: Binucleate cell fusions and hormone production. Placenta 13, 101\u2013113 (1992).","journal-title":"Placenta"},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1530\/rep.1.00340","article-title":"Animal models of implantation","volume":"128","author":"Lee KY","year":"2004","unstructured":"KY Lee, FJ DeMayo, Animal models of implantation. Reproduction 128, 679\u2013695 (2004).","journal-title":"Reproduction"},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1095\/biolreprod43.2.210","article-title":"Expression of trophoblastic interferon genes in sheep and cattle","volume":"43","author":"Farin CE","year":"1990","unstructured":"CE Farin, , Expression of trophoblastic interferon genes in sheep and cattle. Biol Reprod 43, 210\u2013218 (1990).","journal-title":"Biol Reprod"},{"key":"e_1_3_4_42_2","first-page":"432","article-title":"Interferons as hormones of pregnancy","volume":"13","author":"Roberts RM","year":"1992","unstructured":"RM Roberts, JC Cross, DW Leaman, Interferons as hormones of pregnancy. Endocr Rev 13, 432\u2013452 (1992).","journal-title":"Endocr Rev"},{"key":"e_1_3_4_43_2","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1002\/mrd.20496","article-title":"Regulation of conceptus adhesion by endometrial CXC chemokines during the implantation period in sheep","volume":"73","author":"Imakawa K","year":"2006","unstructured":"K Imakawa, , Regulation of conceptus adhesion by endometrial CXC chemokines during the implantation period in sheep. Mol Reprod Dev 73, 850\u2013858 (2006).","journal-title":"Mol Reprod Dev"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.mce.2011.09.035","article-title":"Comparative developmental biology of the uterus: Insights into mechanisms and developmental disruption","volume":"354","author":"Spencer TE","year":"2012","unstructured":"TE Spencer, KA Dunlap, J Filant, Comparative developmental biology of the uterus: Insights into mechanisms and developmental disruption. Mol Cell Endocrinol 354, 34\u201353 (2012).","journal-title":"Mol Cell Endocrinol"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/S0303-7207(01)00697-9","article-title":"Cloning: Experience from the mouse and other animals","volume":"187","author":"Yanagimachi R","year":"2002","unstructured":"R Yanagimachi, Cloning: Experience from the mouse and other animals. Mol Cell Endocrinol 187, 241\u2013248 (2002).","journal-title":"Mol Cell Endocrinol"},{"key":"e_1_3_4_46_2","first-page":"E4","article-title":"Uterine and placental factors regulating conceptus growth in domestic animals","volume":"82","author":"Spencer TE","year":"2004","unstructured":"TE Spencer, FW Bazer, Uterine and placental factors regulating conceptus growth in domestic animals. J Anim Sci 82, E4\u201313 (2004).","journal-title":"J Anim Sci"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btr095","article-title":"Improved structure, function and compatibility for CellProfiler: Modular high-throughput image analysis software","volume":"27","author":"Kamentsky L","year":"2011","unstructured":"L Kamentsky, , Improved structure, function and compatibility for CellProfiler: Modular high-throughput image analysis software. Bioinformatics 27, 1179\u20131180 (2011).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1530\/REP-10-0541","article-title":"Fibroblast growth factors activate mitogen-activated protein kinase pathways to promote migration in ovine trophoblast cells","volume":"141","author":"Yang QE","year":"2011","unstructured":"QE Yang, MI Giassetti, AD Ealy, Fibroblast growth factors activate mitogen-activated protein kinase pathways to promote migration in ovine trophoblast cells. Reproduction 141, 707\u2013714 (2011).","journal-title":"Reproduction"},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1095\/biolreprod.103.020982","article-title":"Cloned cattle fetuses with the same nuclear genetics are more variable than contemporary half-siblings resulting from artificial insemination and exhibit fetal and placental growth deregulation even in the first trimester","volume":"70","author":"Lee RSF","year":"2004","unstructured":"RSF Lee, , Cloned cattle fetuses with the same nuclear genetics are more variable than contemporary half-siblings resulting from artificial insemination and exhibit fetal and placental growth deregulation even in the first trimester. Biol Reprod 70, 1\u201311 (2004).","journal-title":"Biol Reprod"},{"key":"e_1_3_4_50_2","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1016\/S0764-4469(98)80014-0","article-title":"Developmental potential of bovine embryos reconstructed from enucleated matured oocytes fused with cultured somatic cells","volume":"321","author":"Vignon X","year":"1998","unstructured":"X Vignon, , Developmental potential of bovine embryos reconstructed from enucleated matured oocytes fused with cultured somatic cells. C R Acad Sci III 321, 735\u2013745 (1998).","journal-title":"C R Acad Sci III"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1126\/science.1169588","article-title":"The genome sequence of taurine cattle: A window to ruminant biology and evolution","volume":"324","author":"Elsik CG","year":"2009","unstructured":"CG Elsik, , The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science; Bovine Genome Sequencing and Analysis Consortium 324, 522\u2013528 (2009).","journal-title":"Science"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: Discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell C","year":"2009","unstructured":"C Trapnell, L Pachter, SL Salzberg, TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105\u20131111 (2009).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell C","year":"2012","unstructured":"C Trapnell, , Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7, 562\u2013578 (2012).","journal-title":"Nat Protoc"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"Kuhn RM","year":"2013","unstructured":"RM Kuhn, D Haussler, WJ Kent, The UCSC genome browser and associated tools. Brief Bioinform 14, 144\u2013161 (2013).","journal-title":"Brief Bioinform"},{"key":"e_1_3_4_55_2","first-page":"299","article-title":"R: A Language and Environment for Statistical Computing","volume":"5","author":"Ihaka R","year":"2012","unstructured":"R Ihaka, R Gentleman, R: A Language and Environment for Statistical Computing. J Comput Graph Stat 5, 299\u2013314 (2012).","journal-title":"J Comput Graph Stat"},{"key":"e_1_3_4_56_2","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: Open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman RC","year":"2004","unstructured":"RC Gentleman, , Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5, R80 (2004).","journal-title":"Genome Biol"},{"key":"e_1_3_4_57_2","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/S0076-6879(06)11008-3","article-title":"Bioconductor: An open source framework for bioinformatics and computational biology","volume":"411","author":"Reimers M","year":"2006","unstructured":"M Reimers, VJ Carey, Bioconductor: An open source framework for bioinformatics and computational biology. Methods Enzymol 411, 119\u2013134 (2006).","journal-title":"Methods Enzymol"},{"key":"e_1_3_4_58_2","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: An R package for interfacing with genome browsers","volume":"25","author":"Lawrence M","year":"2009","unstructured":"M Lawrence, R Gentleman, V Carey, rtracklayer: An R package for interfacing with genome browsers. Bioinformatics 25, 1841\u20131842 (2009).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_59_2","unstructured":"M Morgan H Pag\u00e9s V Obenchain N Hayden Rsamtools: Binary alignment (BAM) FASTA variant call (BCF) and tabix file import. R package Version 1.26.1. Available at bioconductor.org\/packages\/release\/bioc\/html\/Rsamtools.html. Accessed June 29 2011. (2016)."},{"key":"e_1_3_4_60_2","doi-asserted-by":"crossref","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence M","year":"2013","unstructured":"M Lawrence, , Software for computing and annotating genomic ranges. PLOS Comput Biol 9, e1003118 (2013).","journal-title":"PLOS Comput Biol"},{"key":"e_1_3_4_61_2","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: A Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson MD","year":"2010","unstructured":"MD Robinson, DJ McCarthy, GK Smyth, edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_62_2","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"Robinson MD","year":"2010","unstructured":"MD Robinson, A Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 (2010).","journal-title":"Genome Biol"},{"key":"e_1_3_4_63_2","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"McCarthy DJ","year":"2012","unstructured":"DJ McCarthy, Y Chen, GK Smyth, Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40, 4288\u20134297 (2012).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_64_2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini Y","year":"1995","unstructured":"Y Benjamini, Y Hochberg, Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57, 289\u2013300 (1995).","journal-title":"J R Stat Soc B"},{"key":"e_1_3_4_65_2","doi-asserted-by":"crossref","first-page":"R14","DOI":"10.1186\/gb-2010-11-2-r14","article-title":"Gene ontology analysis for RNA-seq: Accounting for selection bias","volume":"11","author":"Young MD","year":"2010","unstructured":"MD Young, MJ Wakefield, GK Smyth, A Oshlack, Gene ontology analysis for RNA-seq: Accounting for selection bias. 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