Exploring the application of high-throughput genomics technologies in the field of maternal-embryo communication

Theriogenology

Volumn 77, Issue 4, 2012, Pages 717-737

  Almiñana, Carmen ^a   Fazeli, Alireza ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Embryo; High throughput technologies; Maternal tract; Microarrays; Next generation sequencing; Pregnancy

Indexed keywords

COMPLEMENTARY DNA; RNA;

ANIMAL; BREEDING; DNA MICROARRAY; EMBRYO DEVELOPMENT; FEMALE; FEMALE GENITAL SYSTEM; FETOMATERNAL TRANSFUSION; GENE EXPRESSION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; PHYSIOLOGY; PREGNANCY; REVIEW; SEQUENCE ANALYSIS;

ANIMALS; DNA, COMPLEMENTARY; EMBRYONIC DEVELOPMENT; FEMALE; GENE EXPRESSION; GENITALIA, FEMALE; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MATERNAL-FETAL EXCHANGE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREGNANCY; PREGNANCY, ANIMAL; RNA; SEQUENCE ANALYSIS;

EID: 84856689601     PISSN: 0093691X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.theriogenology.2011.11.009     Document Type: Review

References (151)

1. Wolf E., Arnold G.J., Bauersachs S., Beier H.M., Blum H., Einspanier R., et al. Embryo-maternal communication in bovine - Strategies for deciphering a complex cross-talk. Reprod Domest Anim 2003, 38:276-289.
2. Fazeli A. Maternal communication with gametes and embryos. Theriogenology 2008, 70:1182-1187.
3. Fleming T.P., Kwong W.Y., Porter R., Ursell E., Fesenko I., Wilkins A., et al. The embryo and its future. Biol Reprod 2004, 71:1046-1054.
4. Lee K.F., Yao Y.Q., Kwok K.L., Xu J.S., Yeung W.S. Early developing embryos affect the gene expression patterns in the mouse oviduct. Biochem Biophys Res Commun 2002, 292:564-570.
5. Bauersachs S., Ulbrich S.E., Gross K., Schmidt S.E., Meyer H.H., Wenigerkind H., et al. Embryo-induced transcriptome changes in bovine endometrium reveal species-specific and common molecular markers of uterine receptivity. Reproduction 2006, 132:319-331.
6. Klein C., Bauersachs S., Ulbrich S.E., Einspanier R., Meyer H.H., Schmidt S.E., et al. Monozygotic twin model reveals novel embryo-induced transcriptome changes of bovine endometrium in the preattachment period. Biol Reprod 2006, 74:253-264.
7. Klein C., Scoggin K.E., Ealy A.D., Troedsson M.H. Transcriptional profiling of equine endometrium during the time of maternal recognition of pregnancy. Biol Reprod 2010, 83:102-113.
8. Sherwin J.R., Sharkey A.M., Cameo P., Mavrogianis P.M., Catalano R.D., Edassery S., et al. Identification of novel genes regulated by chorionic gonadotropin in baboon endometrium during the window of implantation. Endocrinology 2007, 148:618-626.
9. Green J.A., Kim J.G., Whitworth K.M., Agca C., Prather R.S. The use of microarrays to define functionally-related genes that are differentially expressed in the cycling pig uterus. Soc Reprod Fertil Suppl 2006, 62:163-176.
10. Pan H., Zhu L., Deng Y., Pollard J.W. Microarray analysis of uterine epithelial gene expression during the implantation window in the mouse. Endocrinology 2006, 147:4904-4916.
11. Østrup E., Bauersachs S., Blum H., Wolf E., Hyttel P. Differential endometrial gene expression in pregnant and nonpregnant sows. Biol Reprod 2010, 83:277-285.
12. Walker C.G., Meier S., Littlejohn M.D., Lehnert K., Roche J.R., Mitchell M.D. Modulation of the maternal immune system by the pre-implantation embryo. BMC Genomics 2010, 11:474.
13. Horcajadas J.A., Riesewijk A., Martín J., Cervero A., Mosselman S., Pellicer A., et al. Global gene expression profiling of human endometrial receptivity. J Reprod Immunol 2004, 63:41-49.
14. Hurd P.J., Nelson C.J. Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomics Proteomics 2009, 8:174-183.
15. Fields S. Molecular biology. Site-seeing by sequencing. Science 2007, 316:1441-1442.
16. Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24:133-141.
17. Ansorge W.J. Next-generation DNA sequencing techniques. N Biotechnol 2009, 25:195-203.
18. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323:133-138.
19. Voelkerding K.V., Dames S.A., Durtschi J.D. Next-generation sequencing: From basic research to diagnostics. Clin Chem 2009, 55:641-658.
20. Hocquette J.F. Where are we in genomics?. J Physiol Pharmacol 2005, 56(Suppl 3):37-70.
21. Ridley M. Genome 2006, Harper Perennial, New York, NY.
22. Cassar-Malek I., Picard B., Bernard C., Hocquette J.-F. Application of gene expression studies in livestock production systems: A European perspective. Aust J Exp Agric 2008, 48:701-710.
23. Sun X., Mei S., Tao H., Wang G., Su L., Jiang S., et al. Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows. BMC Genomics 2011, 12:111.
24. Byrne G.W., Du Z., Sun Z., Asmann Y.W., McGregor C.G. Changes in cardiac gene expression after pig-to-primate orthotopic xenotransplantation. Xenotransplantation 2011, 18:14-27.
25. Wang T.H., Lee Y.S., Hwang S.M. Transcriptome analysis of common Gene expression in human mesenchymal stem cells derived from four different origins. Methods Mol Biol 2011, 698:405-417.
26. Gibbs R.A., Taylor J.F., Van Tassell C.P., Barendse W., Eversole K.A., Gill C.A., et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 2009, 324:528-532.
27. Wang H.S., Cheng B.H., Wu H.M., Yen C.F., Liu C.T., Chao A., et al. A mutant single nucleotide polymorphism of follicle-stimulating hormone receptor is associated with a lower risk of endometriosis. Fertil Steril 2011, 95:455-457.
28. Montenegro D., Romero R., Kim S.S., Tarca A.L., Draghici S., Kusanovic J.P., et al. Expression patterns of microRNAs in the chorioamniotic membranes: A role for microRNAs in human pregnancy and parturition. J Pathol 2009, 217:113-121.
29. Liang P., Pardee A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 1992, 257:967-971.
30. Liang P., Pardee A.B. Recent advances in differential display. Curr Opin Immunol 1995, 7:274-280.
31. Sunday M.E. Differential display RT-PCR for identifying novel gene expression in the lung. Am J Physiol 1995, 269:L273-L284.
32. Sompayrac L., Jane S., Burn T.C., Tenen D.G., Danna K.J. Overcoming limitations of the mRNA differential display technique. Nucleic Acids Res 1995, 23:4738-4739.
33. Launer G.A., Lukyanov K.A., Tarabykin V.S., Lukyanov S.A. Simple method for cDNA amplification starting from small amount of total RNA. Mol Genet Mikrobiol Virusol 1994, 38-41.
34. Diatchenko L., Lau Y.F., Campbell A.P., Chenchik A., Moqadam F., Huang B., et al. Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A 1996, 93:6025-6030.
35. Lukyanov K.A., Matz M.V., Bogdanova E.A., Gurskaya N.G., Lukyanov S.A. Molecule by molecule PCR amplification of complex DNA mixtures for direct sequencing: An approach to in vitro cloning. Nucleic Acids Res 1996, 24:2194-2195.
36. Choi S.Y., Jang J.H., Kim K.R. Analysis of differentially expressed genes in human rectal carcinoma using suppression subtractive hybridization. Clin Exp Med 2011, 11:219-226.
37. Pan Z., Chen S., Pan X., Wang Z., Han H., Zheng W., et al. Differential gene expression identified in Uigur women cervical squamous cell carcinoma by suppression subtractive hybridization. Neoplasma 2010, 57:123-128.
38. Zhu L.H., Meng H., Duan X.J., Xu G.Q., Zhang J., Gong D.Q. Gene expression profile in the liver tissue of geese after overfeeding. Poult Sci 2011, 90:107-117.
39. Vallée M., Beaudry D., Roberge C., Matte J.J., Blouin R., Palin M.F. Isolation of differentially expressed genes in conceptuses and endometrial tissue of sows in early gestation. Biol Reprod 2003, 69:1697-1706.
40. Teng X., Xiao H. Perspectives of DNA microarray and next-generation DNA sequencing technologies. Sci China C 2009, 52:7-16.
41. Beattie W.G., Meng L., Turner S.L., Varma R.S., Dao D.D., Beattie K.L. Hybridization of DNA targets to glass-tethered oligonucleotide probes. Mol Biotechnol 1995, 4:213-225.
42. White C.A., Salamonsen L.A. A guide to issues in microarray analysis: Application to endometrial biology. Reproduction 2005, 130:1-13.
43. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
44. McGall G.H., Christians F.C. High-density GeneChip oligonucleotide probe arrays. Adv Biochem Eng/Biotechnol 2002, 77:21-42.
45. Niemann H., Carnwath J.W., Kues W. Application of DNA array technology to mammalian embryos. Theriogenology 2007, 68(Suppl 1):S165-S177.
46. Hardiman G. Microarray platforms-comparisons and contrasts. Pharmacogenomics 2004, 5:487-502.
47. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29:365-371.
48. Rockett J.C., Hellmann G.M. Confirming microarray data-is it really necessary?. Genomics 2004, 83:541-549.
49. Sadikovic B., Yoshimoto M., Al-Romaih K., Maire G., Zielenska M., Squire J.A. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma. PLoS ONE 2008, 3:e2834.
50. Rodriguez B.A., Huang T.H. Tilling the chromatin landscape: Emerging methods for the discovery and profiling of protein-DNA interactions. Biochem Cell Biol 2005, 83:525-534.
51. Rodenhiser D.I., Andrews J., Kennette W., Sadikovic B., Mendlowitz A., Tuck A.B., et al. Epigenetic mapping and functional analysis in a breast cancer metastasis model using whole-genome promoter tiling microarrays. Breast Cancer Res 2008, 10:R62.
52. Velculescu V.E., Zhang L., Vogelstein B., Kinzler K.W. Serial analysis of gene expression. Science 1995, 270:484-487.
53. Brenner S., Johnson M., Bridgham J., Golda G., Lloyd D.H., Johnson D., et al. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000, 18:630-634.
54. Reinartz J., Bruyns E., Lin J.-Z., Burcham T., Brenner S., Bowen B., et al. Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profling in all organisms. Brief Funct Genomics Proteomics 2002, 1:95-104.
55. Sanger F., Coulson A.R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol 1975, 94:441-448.
56. Pariset L., Chillemi G., Bongiorni S., Romano Spica V., Valentini A. Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences. N Biotechnol 2009, 25:272-279.
57. Kircher M., Kelso J. High-throughput DNA sequencing-concepts and limitations. Bioessays 2010, 32:524-536.
58. Marguerat S., Bähler J. RNA-seq: From technology to biology. Cell Mol Life Sci 2010, 67:569-579.
59. Isom S. 243 Gene expression profiling by next-generation sequencing of Cdna samples from inner cell mass and trophectoderm of A Single-Day 12 porcine embryo. Reprod Fertil Dev 2009, 279.
60. Huang W., Khatib H. Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics 2010, 11:711.
61. Metzker M.L. Sequencing technologies - The next generation. Nat Rev Genet 2010, 11:31-46.
62. Shendure J., Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145.
63. Pearson M.M., Sebaihia M., Churcher C., Quail M.A., Seshasayee A.S., Luscombe N.M., et al. Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. J Bacteriol 2008, 190:4027-4037.
64. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456:53-59.
65. Smith D.R., Quinlan A.R., Peckham H.E., Makowsky K., Tao W., Woolf B., et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 2008, 18:1638-1642.
66. Satkoski J.A., Malhi R., Kanthaswamy S., Tito R., Malladi V., Smith D. Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta). BMC Genomics 2008, 9:256.
67. Ding G., Zhang D., Feng Z., Fan W., Ding X., Li X., et al. SNP, ARMS and SSH authentication of medicinal Dendrobium officinale KIMURA et MIGO and application for identification of Fengdou drugs. Biol Pharm Bull 2008, 31:553-557.
68. Yeager M., Xiao N., Hayes R.B., Bouffard P., Desany B., Burdett L., et al. Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Hum Genet 2008, 124:161-170.
69. Ding Y., Larson G., Rivas G., Lundberg C., Geller L., Ouyang C., et al. Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk. PLoS ONE 2008, 3:e3533.
70. Campbell P.J., Stephens P.J., Pleasance E.D., O'Meara S., Li H., Santarius T., et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008, 40:722-729.
71. Kim H.R., Shin M.G., Kim M.J., Kim H.J., Shin J.H., Suh S.P., et al. Mitochondrial DNA aberrations of bone marrow cells from patients with aplastic anemia. J Korean Med Sci 2008, 23:1062-1067.
72. Wang Z., Gerstein M., Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
73. Wold B., Myers R.M. Sequence census methods for functional genomics. Nat Methods 2008, 5:19-21.
74. Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415.
75. Simon S.A., Zhai J., Nandety R.S., McCormick K.P., Zeng J., Mejia D., et al. Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Biol 2009, 60:305-333.
76. Patino W.D., Mian O.Y., Hwang P.M. Serial analysis of gene expression: Technical considerations and applications to cardiovascular biology. Circ Res 2002, 91:565-569.
77. Wang L., Li P., Brutnell T.P. Exploring plant transcriptomes using ultra high-throughput sequencing. Brief Funct. Genomics 2010, 9:118-128.
78. Nagalakshmi U., Wang Z., Waern K., Shou C., Raha D., Gerstein M., et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349.
79. Sultan M., Schulz M.H., Richard H., Magen A., Klingenhoff A., Scherf M., et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
80. Sultan M.Z., Jeon Y.M., Moon S.S. Labdane-type diterpenes active against acne from pine cones (Pinus densiflora). Planta Med 2008, 74:449-452.
81. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628.
82. Kuo M.H., Allis C.D. In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods 1999, 19:425-433.
83. Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309.
84. Farnham P.J. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616.
85. Johnson D.S., Mortazavi A., Myers R.M., Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502.
86. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
87. Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
88. Chiu R.W., Chan K.C., Gao Y., Lau V.Y., Zheng W., Leung T.Y., et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci U S A 2008, 105:20458-20463.
89. Fan H.C., Blumenfeld Y.J., Chitkara U., Hudgins L., Quake S.R. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A 2008, 105:16266-16271.
90. Harris T.D., Buzby P.R., Babcock H., Beer E., Bowers J., Braslavsky I., et al. Single-molecule DNA sequencing of a viral genome. Science 2008, 320:106-109.
91. Korlach J., Bjornson K.P., Chaudhuri B.P., Cicero R.L., Flusberg B.A., Gray J.J., et al. Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 2010, 472:431-455.
92. Clarke J., Wu H.C., Jayasinghe L., Patel A., Reid S., Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 2009, 4:265-270.
93. Dahl F., Stenberg J., Fredriksson S., Welch K., Zhang M., Nilsson M., et al. Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Natl Acad Sci U S A 2007, 104:9387-9392.
94. Albert T.J., Molla M.N., Muzny D.M., Nazareth L., Wheeler D., Song X., et al. Direct selection of human genomic loci by microarray hybridization. Nat Methods 2007, 4:903-905.
95. Chang H.S., Cheng W.T., Wu H.K., Choo K.B. Identification of genes expressed in the epithelium of porcine oviduct containing early embryos at various stages of development. Mol Reprod Dev 2000, 56:331-335.
96. Lee K.F., Kwok K.L., Yeung W.S. Suppression subtractive hybridization identifies genes expressed in oviduct during mouse preimplantation period. Biochem Biophys Res Commun 2000, 277:680-685.
97. Lee K.F., Kwok K.L., Chung M.K., Lee Y.L., Chow J.F., Yeung W.S. Phospholipid transfer protein (PLTP) mRNA expression is stimulated by developing embryos in the oviduct. J Cell Biochem 2005, 95:740-749.
98. Wilcox A.J., Baird D.D., Weinberg C.R. Time of implantation of the conceptus and loss of pregnancy. N Engl J Med 1999, 340:1796-1799.
99. Margalioth E.J., Ben-Chetrit A., Gal M., Eldar-Geva T. Investigation and treatment of repeated implantation failure following IVF-ET. Hum Reprod 2006, 21:3036-3043.
100. Chen Y., Antoniou E., Liu Z., Hearne L.B., Roberts R.M. A microarray analysis for genes regulated by interferon-tau in ovine luminal epithelial cells. Reproduction 2007, 134:123-135.
101. Forde N., Carter F., Fair T., Crowe M.A., Evans A.C., Spencer T.E., et al. Progesterone-regulated changes in endometrial gene expression contribute to advanced conceptus development in cattle. Biol Reprod 2009, 81:784-794.
102. Saberi A.A., Niry M.D., Fazeli S.M., Rahimi Tabar M.R., Rouhani S. Conformal invariance of isoheight lines in a two-dimensional Kardar-Parisi-Zhang surface. Phys Rev E Stat Nonlin Soft Matter Phys 2008, 77:051607.
103. Satterfield M.C., Song G., Kochan K.J., Riggs P.K., Simmons R.M., Elsik C.G., et al. Discovery of candidate genes and pathways in the endometrium regulating ovine blastocyst growth and conceptus elongation. Physiol Genomics 2009, 39:85-99.
104. Tapia A., Gangi L.M., Zegers-Hochschild F., Balmaceda J., Pommer R., Trejo L., et al. Differences in the endometrial transcript profile during the receptive period between women who were refractory to implantation and those who achieved pregnancy. Hum Reprod 2008, 23:340-351.
105. Altmäe S., Martínez-Conejero J.A., Salumets A., Simón C., Horcajadas J.A., Stavreus-Evers A. Endometrial gene expression analysis at the time of embryo implantation in women with unexplained infertility. Mol Hum Reprod 2010, 16:178-187.
106. Díaz-Gimeno P., Horcajadas J.A., Martínez-Conejero J.A., Esteban F.J., Alamá P., Pellicer A., et al. A genomic diagnostic tool for human endometrial receptivity based on the transcriptomic signature. Fertil Steril 2011, 95:50-60.
107. Haouzi D., Assou S., Mahmoud K., Tondeur S., Rème T., Hedon B., et al. Gene expression profile of human endometrial receptivity: Comparison between natural and stimulated cycles for the same patients. Hum Reprod 2009, 24:1436-1445.
108. Paidas M.J., Krikun G., Huang S.J., Jones R., Romano M., Annunziato J., et al. A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells. Am J Obstet Gynecol 2010, 202:e451-e458.
109. Robert C. Microarray analysis of gene expression during early development: A cautionary overview. Reproduction 2010, 140:787-801.
110. Bauersachs S., Mitko K., Blum H., Wolf E. Technical note: Bovine oviduct and endometrium array version 1: A tailored tool for studying bovine endometrium biology and pathophysiology. J Dairy Sci 2007, 90:4420-4423.
111. Dey S.K., Lim H., Das S.K., Reese J., Paria B.C., Daikoku T., et al. Molecular cues to implantation. Endocr Rev 2004, 25:341-373.
112. Paria B.C., Reese J., Das S.K., Dey S.K. Deciphering the cross-talk of implantation: Advances and challenges. Science 2002, 296:2185-2188.
113. Hamatani T., Carter M.G., Sharov A.A., Ko M.S. Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell 2004, 6:117-131.
114. Wang Q.T., Piotrowska K., Ciemerych M.A., Milenkovic L., Scott M.P., Davis R.W., et al. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev Cell 2004, 6:133-144.
115. Ushizawa K., Herath C.B., Kaneyama K., Shiojima S., Hirasawa A., Takahashi T., et al. cDNA microarray analysis of bovine embryo gene expression profiles during the pre-implantation period. Reprod Biol Endocrinol 2004, 2:77.
116. Adjaye J., Herwig R., Brink T.C., Herrmann D., Greber B., Sudheer S., et al. Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression. Physiol Genomics 2007, 31:315-327.
117. Assou S., Haouzi D., De Vos J., Hamamah S. Human cumulus cells as biomarkers for embryo and pregnancy outcomes. Mol Hum Reprod 2010, 16:531-538.
118. Niemann H., Wrenzycki C. Alterations of expression of developmentally important genes in preimplantation bovine embryos by in vitro culture conditions: Implications for subsequent development. Theriogenology 2000, 53:21-34.
119. Wrenzycki C., Herrmann D., Lucas-Hahn A., Gebert C., Korsawe K., Lemme E., et al. Epigenetic reprogramming throughout preimplantation development and consequences for assisted reproductive technologies. Birth Defects Res C Embryo Today 2005, 75:1-9.
120. Wrenzycki C., Herrmann D., Lucas-Hahn A., Korsawe K., Lemme E., Niemann H. Messenger RNA expression patterns in bovine embryos derived from in vitro procedures and their implications for development. Reprod Fertil Dev 2005, 17:23-35.
121. Corcoran D., Fair T., Park S., Rizos D., Patel O.V., Smith G.W., et al. Suppressed expression of genes involved in transcription and translation in in vitro compared with in vivo cultured bovine embryos. Reproduction 2006, 131:651-660.
122. Pfister-Genskow M., Myers C., Childs L.A., Lacson J.C., Patterson T., Betthauser J.M., et al. Identification of differentially expressed genes in individual bovine preimplantation embryos produced by nuclear transfer: Improper reprogramming of genes required for development. Biol Reprod 2005, 72:546-555.
123. Smith S.L., Everts R.E., Tian X.C., Du F., Sung L.Y., Rodriguez-Zas S.L., et al. Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning. Proc Natl Acad Sci U S A 2005, 102:17582-17587.
124. Somers J., Smith C., Donnison M., Wells D.N., Henderson H., McLeay L., et al. Gene expression profiling of individual bovine nuclear transfer blastocysts. Reproduction 2006, 131:1073-1084.
125. Sásik R., Woelk C.H., Corbeil J. Microarray truths and consequences. J Mol Endocrinol 2004, 33:1-9.
126. Quackenbush J. Microarray data normalization and transformation. Nat Genet 2002, 32(Suppl):496-501.
127. Te Pas M.F., van Hemert S., Hulsegge B., Hoekman A.J., Pool M.H., Rebel J.M., et al. A pathway analysis tool for analyzing microarray data of species with low physiological information. Adv. Bioinformatics 2008, 719468.
128. Jirtle R.L., Skinner M.K. Environmental epigenomics and disease susceptibility. Nat Rev Genet 2007, 8:253-262.
129. Hu S.J., Ren G., Liu J.L., Zhao Z.A., Yu Y.S., Su R.W., et al. MicroRNA expression and regulation in mouse uterus during embryo implantation. J Biol Chem 2008, 283:23473-23484.
130. Revil T., Gaffney D., Dias C., Majewski J., Jerome-Majewska L.A. Alternative splicing is frequent during early embryonic development in mouse. BMC Genomics 2010, 11:399.
131. Donaldson L., Vuocolo T., Gray C., Strandberg Y., Reverter A., McWilliam S., et al. Construction and validation of a bovine innate immune microarray. BMC Genomics 2005, 6:135.
132. Burkitt M., Walker D., Romano D.M., Fazeli A. Constructing complex 3D biological environments from medical imaging using high performance computing. IEEE/ACM Trans Comput Biol Bioinform 2011.
133. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
134. Nielsen K.L., Høgh A.L., Emmersen J. DeepSAGE-digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucleic Acids Res 2006, 34:e133.
135. Lau S.K., Ng K.H., Woo P.C., Yip K.T., Fung A.M., Woo G.K., et al. Usefulness of the MicroSeq 500 16S rDNA bacterial identification system for identification of anaerobic gram positive bacilli isolated from blood cultures. J Clin Pathol 2006, 59:219-222.
136. Houwing S., Kamminga L.M., Berezikov E., Cronembold D., Girard A., van den Elst H., et al. A role for piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 2007, 129:69-82.
137. Morin R.D., O'Connor M.D., Griffith M., Kuchenbauer F., Delaney A., Prabhu A.L., et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 2008, 18:610-621.
138. Mikkelsen T.S., Wakefield M.J., Aken B., Amemiya C.T., Chang J.L., Duke S., et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007, 447:167-177.
139. Kertesz M., Wan Y., Mazor E., Rinn J.L., Nutter R.C., Chang H.Y., et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467:103-107.
140. Leary R.J., Kinde I., Diehl F., Schmidt K., Clouser C., Duncan C., et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2010, 2. 20ra14.
141. Graveley B.R., Brooks A.N., Carlson J.W., Duff M.O., Landolin J.M., Yang L., et al. The developmental transcriptome of Drosophila melanogaster. Nature 2011, 471:473-479.
142. Goren A., Ozsolak F., Shoresh N., Ku M., Adli M., Hart C., et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 2010, 7:47-49.
143. Ozsolak F., Platt A.R., Jones D.R., Reifenberger J.G., Sass L.E., McInerney P., et al. Direct RNA sequencing. Nature 2009, 461:814-818.
144. Ka H., Seo H., Kim M., Moon S., Kim H., Lee C.K. Gene expression profiling of the uterus with embryos cloned by somatic cell nuclear transfer on day 30 of pregnancy. Anim Reprod Sci 2008, 108:79-91.
145. Bauersachs S., Ulbrich S.E., Zakhartchenko V., Minten M., Reichenbach M., Reichenbach H.D., et al. The endometrium responds differently to cloned versus fertilized embryos. Proc Natl Acad Sci U S A 2009, 106:5681-5686.
146. Mansouri-Attia N., Sandra O., Aubert J., Degrelle S., Everts R.E., Giraud-Delville C., et al. Endometrium as an early sensor of in vitro embryo manipulation technologies. Proc Natl Acad Sci U S A 2009, 106:5687-5692.
147. Merkl M., Ulbrich S.E., Otzdorff C., Herbach N., Wanke R., Wolf E., et al. Microarray analysis of equine endometrium at days 8 and 12 of pregnancy. Biol Reprod 2010, 83:874-886.
148. Miles J.R., Blomberg L.A., Krisher R.L., Everts R.E., Sonstegard T.S., Van Tassell C.P., et al. Comparative transcriptome analysis of in vivo- and in vitro-produced porcine blastocysts by small amplified RNA-serial analysis of gene expression (SAR-SAGE). Mol Reprod Dev 2008, 75:976-988.
149. Ross J.W., Ashworth M.D., Stein D.R., Couture O.P., Tuggle C.K., Geisert R.D. Identification of differential gene expression during porcine conceptus rapid trophoblastic elongation and attachment to uterine luminal epithelium. Physiol Genomics 2009, 36:140-148.
150. Blomberg le A., Schreier L., Li R.W. Characteristics of peri-implantation porcine concepti population and maternal milieu influence the transcriptome profile. Mol Reprod Dev 2010, 77:978-989.
151. Isom S.C., Spollen W.G., Blake S.M., Bauer B.K., Springer G.K., Prather R.S. Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra-deep sequencing technologies. Mol Reprod Dev 2010, 77:812-819.