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Volumn 13, Issue 1, 2012, Pages

RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts

Author keywords

Alternative splicing; In vitro fertilization; In vivo embryo; RNA Seq; Transcriptome

Indexed keywords

CHOLESTEROL; MESSENGER RNA; TRANSCRIPTOME;

EID: 84858958588     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-118     Document Type: Article
Times cited : (105)

References (43)
  • 1
    • 84867401242 scopus 로고    scopus 로고
    • IETS 2011 Statistics and Data Retrieval Committee Report The year 2010 worldwide statistics of embryo transfer in domestic farm animals
    • Stroud B. IETS 2011 Statistics and Data Retrieval Committee Report The year 2010 worldwide statistics of embryo transfer in domestic farm animals. Embryo Transfer Newsletter 2011, 29:1-23.
    • (2011) Embryo Transfer Newsletter , vol.29 , pp. 1-23
    • Stroud, B.1
  • 2
    • 84861870150 scopus 로고    scopus 로고
    • CDC- Assisted Reproductive Technology
    • CDC- Assisted Reproductive Technology CDC- Assisted Reproductive Technology., http://www.cdc.gov/art/
  • 3
    • 79956370834 scopus 로고    scopus 로고
    • International Committee for Monitoring Assisted Reproductive Technology (ICMART) world report: assisted reproductive technology 2003
    • 10.1016/j.fertnstert.2011.03.058, 21536284
    • Nygren K, Sullivan E, Zegers-Hochschild F, Mansour T, Ishihara O, Adamson D, de Mouzon J. International Committee for Monitoring Assisted Reproductive Technology (ICMART) world report: assisted reproductive technology 2003. Fertil Steril 2011, 95:2209-2222.e17. 10.1016/j.fertnstert.2011.03.058, 21536284.
    • (2011) Fertil Steril , vol.95
    • Nygren, K.1    Sullivan, E.2    Zegers-Hochschild, F.3    Mansour, T.4    Ishihara, O.5    Adamson, D.6    de Mouzon, J.7
  • 4
    • 28044455263 scopus 로고    scopus 로고
    • Errors in development of fetuses and placentas from in vitro-produced bovine embryos
    • Farin PW, Piedrahita JA, Farin CE. Errors in development of fetuses and placentas from in vitro-produced bovine embryos. Theriogenology 2006, 5:178-191.
    • (2006) Theriogenology , vol.5 , pp. 178-191
    • Farin, P.W.1    Piedrahita, J.A.2    Farin, C.E.3
  • 5
    • 15844423514 scopus 로고    scopus 로고
    • Ex vivo early embryo development and effects on gene expression and imprinting
    • 10.1071/RD04103, 15745644
    • Gardner DK, Lane M. Ex vivo early embryo development and effects on gene expression and imprinting. Reprod Fertil Dev 2005, 17:361-370. 10.1071/RD04103, 15745644.
    • (2005) Reprod Fertil Dev , vol.17 , pp. 361-370
    • Gardner, D.K.1    Lane, M.2
  • 6
  • 7
    • 0035163469 scopus 로고    scopus 로고
    • Ultrastructure of bovine blastocysts following cryopreservation: effect of method of blastocyst production
    • 10.1002/1098-2795(200102)58:2<186::AID-MRD8>3.0.CO;2-N, 11139231
    • Fair T, Lonergan P, Dinnyes A, Cottell DC, Hyttel P, Ward FA, Boland MP. Ultrastructure of bovine blastocysts following cryopreservation: effect of method of blastocyst production. Mol Reprod Dev 2001, 58:186-195. 10.1002/1098-2795(200102)58:2<186::AID-MRD8>3.0.CO;2-N, 11139231.
    • (2001) Mol Reprod Dev , vol.58 , pp. 186-195
    • Fair, T.1    Lonergan, P.2    Dinnyes, A.3    Cottell, D.C.4    Hyttel, P.5    Ward, F.A.6    Boland, M.P.7
  • 8
    • 0035030576 scopus 로고    scopus 로고
    • Ultrastructural morphometry of bovine blastocysts produced in vivo or in vitro
    • 10.1095/biolreprod64.5.1375, 11319141
    • Crosier AE, Farin PW, Dykstra MJ, Alexander JE, Farin CE. Ultrastructural morphometry of bovine blastocysts produced in vivo or in vitro. Biol Reprod 2001, 64:1375-1385. 10.1095/biolreprod64.5.1375, 11319141.
    • (2001) Biol Reprod , vol.64 , pp. 1375-1385
    • Crosier, A.E.1    Farin, P.W.2    Dykstra, M.J.3    Alexander, J.E.4    Farin, C.E.5
  • 9
    • 0036015191 scopus 로고    scopus 로고
    • Developmental, qualitative, and ultrastructural differences between ovine and bovine embryos produced in vivo or in vitro
    • 10.1002/mrd.10138, 12112595
    • Rizos D, Fair T, Papadopoulos S, Boland MP, Longergan P. Developmental, qualitative, and ultrastructural differences between ovine and bovine embryos produced in vivo or in vitro. Mol Reprod Dev 2002, 62:320-327. 10.1002/mrd.10138, 12112595.
    • (2002) Mol Reprod Dev , vol.62 , pp. 320-327
    • Rizos, D.1    Fair, T.2    Papadopoulos, S.3    Boland, M.P.4    Longergan, P.5
  • 10
    • 0034075868 scopus 로고    scopus 로고
    • Energy metabolism in preimplantation bovine embryos derived in vitro or in vivo
    • 10.1095/biolreprod62.4.847, 10727252
    • Khurana NK, Niemann H. Energy metabolism in preimplantation bovine embryos derived in vitro or in vivo. Biol Reprod 2000, 62:847-856. 10.1095/biolreprod62.4.847, 10727252.
    • (2000) Biol Reprod , vol.62 , pp. 847-856
    • Khurana, N.K.1    Niemann, H.2
  • 12
    • 0035024267 scopus 로고    scopus 로고
    • Effects of culture system and protein supplementation on mRNA expression in pre-implantation bovine embryos
    • 10.1093/humrep/16.5.893, 11331635
    • Wrenzycki C, Herrmann D, Keskintepe L, Martins A, Sirisathien S, Brackett B, Niemann H. Effects of culture system and protein supplementation on mRNA expression in pre-implantation bovine embryos. Hum Reprod 2001, 16:893-901. 10.1093/humrep/16.5.893, 11331635.
    • (2001) Hum Reprod , vol.16 , pp. 893-901
    • Wrenzycki, C.1    Herrmann, D.2    Keskintepe, L.3    Martins, A.4    Sirisathien, S.5    Brackett, B.6    Niemann, H.7
  • 14
    • 58149380723 scopus 로고    scopus 로고
    • Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo
    • 10.1073/pnas.0805616105, 2604955, 19064908
    • Kues WA, Sudheer S, Herrmann D, Carnwath JW, Havlicek V, Besenfelder U, Lehrach H, Adjaye J, Niemann H. Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo. Proc Natl Acad Sci USA 2008, 105:19768-19773. 10.1073/pnas.0805616105, 2604955, 19064908.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 19768-19773
    • Kues, W.A.1    Sudheer, S.2    Herrmann, D.3    Carnwath, J.W.4    Havlicek, V.5    Besenfelder, U.6    Lehrach, H.7    Adjaye, J.8    Niemann, H.9
  • 16
    • 33749245906 scopus 로고    scopus 로고
    • Zygote donor nitrogen metabolism and in vitro embryo culture perturbs in utero development and IGF2R expression in ovine fetal tissues
    • 10.1016/j.theriogenology.2006.05.008, 16777210
    • Powell K, Rooke JA, McEvoy TG, Ashworth CJ, Robinson JJ, Wilmut I, Young LE, Sinclair KD. Zygote donor nitrogen metabolism and in vitro embryo culture perturbs in utero development and IGF2R expression in ovine fetal tissues. Theriogenology 2006, 66:1901-1912. 10.1016/j.theriogenology.2006.05.008, 16777210.
    • (2006) Theriogenology , vol.66 , pp. 1901-1912
    • Powell, K.1    Rooke, J.A.2    McEvoy, T.G.3    Ashworth, C.J.4    Robinson, J.J.5    Wilmut, I.6    Young, L.E.7    Sinclair, K.D.8
  • 17
    • 34547843538 scopus 로고    scopus 로고
    • Effect of in vitro fertilization on gene expression and development of mouse preimplantation embryos
    • 10.1530/REP-06-0247, 17641089
    • Giritharan G, Talbi S, Donjacour A, Di Sebastiano F, Dobson AT, Rinaudo PF. Effect of in vitro fertilization on gene expression and development of mouse preimplantation embryos. Reproduction 2007, 134:63-72. 10.1530/REP-06-0247, 17641089.
    • (2007) Reproduction , vol.134 , pp. 63-72
    • Giritharan, G.1    Talbi, S.2    Donjacour, A.3    Di Sebastiano, F.4    Dobson, A.T.5    Rinaudo, P.F.6
  • 18
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 19
    • 84870647022 scopus 로고    scopus 로고
    • UCSC Genome Browser
    • UCSC Genome Browser. , http://genome.ucsc.edu/
  • 20
    • 77957279300 scopus 로고    scopus 로고
    • Next generation sequencing in functional genomics
    • 10.1093/bib/bbq018, 20501549
    • Werner T. Next generation sequencing in functional genomics. Brief Bioinform 2010, 11:499-511. 10.1093/bib/bbq018, 20501549.
    • (2010) Brief Bioinform , vol.11 , pp. 499-511
    • Werner, T.1
  • 22
    • 79960631411 scopus 로고    scopus 로고
    • Differential expression of heat shock protein genes and their splice variants in bovine preimplantation embryos
    • 10.3168/jds.2010-4137, 21787952
    • Zhang B, Peñagaricano F, Driver A, Chen H, Khatib H. Differential expression of heat shock protein genes and their splice variants in bovine preimplantation embryos. J Dairy Sci 2011, 94:4174-4182. 10.3168/jds.2010-4137, 21787952.
    • (2011) J Dairy Sci , vol.94 , pp. 4174-4182
    • Zhang, B.1    Peñagaricano, F.2    Driver, A.3    Chen, H.4    Khatib, H.5
  • 23
    • 33746095457 scopus 로고    scopus 로고
    • The use of Dhcr7 knockout mouse to accurately determine the origin of fetal sterols
    • 10.1194/jlr.M600141-JLR200, 1488821, 16651660
    • Tint GS, Yu H, Shang Q, Xu G, Patel SB. The use of Dhcr7 knockout mouse to accurately determine the origin of fetal sterols. J Lipid Res 2006, 47:1535-1541. 10.1194/jlr.M600141-JLR200, 1488821, 16651660.
    • (2006) J Lipid Res , vol.47 , pp. 1535-1541
    • Tint, G.S.1    Yu, H.2    Shang, Q.3    Xu, G.4    Patel, S.B.5
  • 24
    • 37249040886 scopus 로고    scopus 로고
    • Histone Deacetylase 3 Down-regulates Cholesterol Synthesis through Repression of Lanosterol Synthase Gene Expression
    • Villagra A, Ulloa N, Zhang X, Zhigang Y, Sotomayor E, Seto E. Histone Deacetylase 3 Down-regulates Cholesterol Synthesis through Repression of Lanosterol Synthase Gene Expression. J Bio Chem 2007, 282:35457-35470.
    • (2007) J Bio Chem , vol.282 , pp. 35457-35470
    • Villagra, A.1    Ulloa, N.2    Zhang, X.3    Zhigang, Y.4    Sotomayor, E.5    Seto, E.6
  • 25
    • 79961118496 scopus 로고    scopus 로고
    • Regulation of HMG-CoA reductase in mammals and yeast
    • 10.1016/j.plipres.2011.07.002, 21801748
    • Burg S, Espenshade P. Regulation of HMG-CoA reductase in mammals and yeast. Prog Lipid Res 2011, 50:403-410. 10.1016/j.plipres.2011.07.002, 21801748.
    • (2011) Prog Lipid Res , vol.50 , pp. 403-410
    • Burg, S.1    Espenshade, P.2
  • 26
    • 78049241914 scopus 로고    scopus 로고
    • Regulation of early trophoblast differentiation- lessons from the mouse
    • 10.1016/j.placenta.2010.07.013, 20797785
    • Senner CE, Hemberger M. Regulation of early trophoblast differentiation- lessons from the mouse. Placenta 2010, 31:944-950. 10.1016/j.placenta.2010.07.013, 20797785.
    • (2010) Placenta , vol.31 , pp. 944-950
    • Senner, C.E.1    Hemberger, M.2
  • 27
    • 0024803783 scopus 로고
    • In vitro culture of bovine egg fertilized either in vitro or in vivo
    • 10.1051/rnd:19890505, 2604870
    • Marquant-Le Guienne B, Gerard M, Solari A, Thibault C. In vitro culture of bovine egg fertilized either in vitro or in vivo. Reprod Nutr Dev 1989, 29:559-568. 10.1051/rnd:19890505, 2604870.
    • (1989) Reprod Nutr Dev , vol.29 , pp. 559-568
    • Marquant-Le Guienne, B.1    Gerard, M.2    Solari, A.3    Thibault, C.4
  • 28
    • 78650140999 scopus 로고    scopus 로고
    • Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq
    • 10.1186/1471-2164-11-711, 3019235, 21167046
    • Huang W, Khatib H. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics 2010, 11:711. 10.1186/1471-2164-11-711, 3019235, 21167046.
    • (2010) BMC Genomics , vol.11 , pp. 711
    • Huang, W.1    Khatib, H.2
  • 29
    • 0036490363 scopus 로고    scopus 로고
    • Mouse and bovine models for human IVF
    • 10.1016/S1472-6483(10)61936-0, 12470581
    • Menezo Y, Herubel F. Mouse and bovine models for human IVF. Reprod BioMed Online 2002, 4:170-175. 10.1016/S1472-6483(10)61936-0, 12470581.
    • (2002) Reprod BioMed Online , vol.4 , pp. 170-175
    • Menezo, Y.1    Herubel, F.2
  • 30
    • 44949215586 scopus 로고    scopus 로고
    • A new presynchronization system (Double-Ovsynch) increases fertility at first postpartum timed AI in lactating dairy cows
    • 10.1016/j.theriogenology.2008.03.014, 18468675
    • Souza AH, Ayres H, Ferreira RM, Wiltbank MC. A new presynchronization system (Double-Ovsynch) increases fertility at first postpartum timed AI in lactating dairy cows. Theriogenology 2008, 70:208-215. 10.1016/j.theriogenology.2008.03.014, 18468675.
    • (2008) Theriogenology , vol.70 , pp. 208-215
    • Souza, A.H.1    Ayres, H.2    Ferreira, R.M.3    Wiltbank, M.C.4
  • 31
    • 78649642153 scopus 로고    scopus 로고
    • Effect of dietary organic zinc, manganese, copper, and cobalt supplementation on milk production, follicular growth, embryo quality, and tissue mineral concentrations in dairy cows
    • 10.2527/jas.2010-3055, 20817861
    • Hackbart KS, Ferreira RM, Dietsche AA, Socha MT, Shaver RD, Wiltbank MC, Fricke PM. Effect of dietary organic zinc, manganese, copper, and cobalt supplementation on milk production, follicular growth, embryo quality, and tissue mineral concentrations in dairy cows. J Anim Sci 2010, 88:3856-3870. 10.2527/jas.2010-3055, 20817861.
    • (2010) J Anim Sci , vol.88 , pp. 3856-3870
    • Hackbart, K.S.1    Ferreira, R.M.2    Dietsche, A.A.3    Socha, M.T.4    Shaver, R.D.5    Wiltbank, M.C.6    Fricke, P.M.7
  • 33
    • 39049119431 scopus 로고    scopus 로고
    • Mutations in the STAT5A Gene Are Associated with Embryonic Survival and Milk Composition in Cattle
    • 10.3168/jds.2007-0669, 18218766
    • Khatib H, Monson RL, Schutzkus V, Kohl DM, Rosa GJM, Rutledge JJ. Mutations in the STAT5A Gene Are Associated with Embryonic Survival and Milk Composition in Cattle. J Dairy Sci 2008, 91:784-793. 10.3168/jds.2007-0669, 18218766.
    • (2008) J Dairy Sci , vol.91 , pp. 784-793
    • Khatib, H.1    Monson, R.L.2    Schutzkus, V.3    Kohl, D.M.4    Rosa, G.J.M.5    Rutledge, J.J.6
  • 34
    • 0000197274 scopus 로고
    • Effect of bovine sperm separation by either swim-up or Percoll method on success of in vitro fertilization and early embryonic development
    • 10.1016/0093-691X(95)00271-9, 16727781
    • Parrish JJ, Krogenaes A, Susko-Parrish JL. Effect of bovine sperm separation by either swim-up or Percoll method on success of in vitro fertilization and early embryonic development. Theriogenology 1995, 44:859-869. 10.1016/0093-691X(95)00271-9, 16727781.
    • (1995) Theriogenology , vol.44 , pp. 859-869
    • Parrish, J.J.1    Krogenaes, A.2    Susko-Parrish, J.L.3
  • 35
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • 10.1186/gb-2010-11-8-r86, 2945788, 20738864
    • Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11:R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
    • (2010) Genome Biol , vol.11
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 36
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • 10.1038/nbt.1621, 3146043, 20436464
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28:511-515. 10.1038/nbt.1621, 3146043, 20436464.
    • (2010) Nature Biotechnology , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    van Baren, M.J.6    Salzberg, S.L.7    Wold, B.J.8    Pachter, L.9
  • 37
    • 79952709611 scopus 로고    scopus 로고
    • Improving RNA-Seq expression estimates by correcting for fragment bias
    • 10.1186/gb-2011-12-3-r22, 3129672, 21410973
    • Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 2011, 12:R22. 10.1186/gb-2011-12-3-r22, 3129672, 21410973.
    • (2011) Genome Biol , vol.12
    • Roberts, A.1    Trapnell, C.2    Donaghey, J.3    Rinn, J.L.4    Pachter, L.5
  • 38
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033, 2832824, 20110278
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 39
    • 0001677717 scopus 로고
    • Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing
    • Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. J R Statist Soc B 1995, 57:963-971.
    • (1995) J R Statist Soc B , vol.57 , pp. 963-971
    • Benjamini, Y.1    Hochberg, Y.2
  • 40
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: accounting for selection bias
    • 10.1186/gb-2010-11-2-r14, 2872874, 20132535
    • Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 2010, 11:R14. 10.1186/gb-2010-11-2-r14, 2872874, 20132535.
    • (2010) Genome Biol , vol.11
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4
  • 41
    • 70149113077 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team
    • R Development Core Team R: A Language and Environment for Statistical Computing 2009, Vienna, Austria: R Foundation for Statistical Computing, R Development Core Team.
    • (2009) R: A Language and Environment for Statistical Computing
  • 42
    • 0037129827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • 126239, 12184808
    • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:research0034. 126239, 12184808.
    • (2002) Genome Biol , vol.3
    • Vandesompele, J.1    De Preter, K.2    Pattyn, F.3    Poppe, B.4    Van Roy, N.5    De Paepe, A.6    Speleman, F.7
  • 43
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method
    • 10.1006/meth.2001.1262, 11846609
    • Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt method. Methods 2001, 25:402-408. 10.1006/meth.2001.1262, 11846609.
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2


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