Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Jäger, Marten ^a   Ott, Claus Eric ^a   Grünhagen, Johannes ^a   Hecht, Jochen ^a,b   Schell, Hanna ^a   Mundlos, Stefan ^a,b   Duda, Georg N ^a   Robinson, Peter N ^a,b   Lienau, Jasmin ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ANIMAL EXPERIMENT; ANIMAL GENETICS; ANIMAL TISSUE; ARTICLE; EXPERIMENTAL MODEL; EXPRESSED SEQUENCE TAG; FEMALE; FRACTURE HEALING; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE MAPPING; GENETIC TRANSCRIPTION; HEALING IMPAIRMENT; NONHUMAN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SHEEP; TIBIA OSTEOTOMY; TRANSCRIPTOMICS; ANIMAL; BIOLOGY; BONE; CATTLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; DISEASE MODEL; DNA SEQUENCE; GENETICS; METABOLISM; METHODOLOGY; MOUSE;

ANIMALIA; OVIS; OVIS ARIES;

ANIMALS; BONE AND BONES; CATTLE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DISEASE MODELS, ANIMAL; FEMALE; FRACTURE HEALING; GENE EXPRESSION PROFILING; MICE; SEQUENCE ANALYSIS, DNA; SHEEP, DOMESTIC;

EID: 79953102823     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-158     Document Type: Article

References (50)

1. Shofti R, Zaretzki A, Cohen E, Engel A, Bar-El Y. The sheep as a model for coronary artery bypass surgery. Lab Anim 2004, 38(2):149-157. 10.1258/002367704322968821, 15070454.
2. Matsuzaki K, Morita M, Hamamoto H, Noma M, Robb JD, Gillespie MJ, Gorman JH, Gorman RC. Elimination of Ischemic Mitral Regurgitation Does Not Alter Long-Term Left Ventricular Remodeling in the Ovine Model. Ann Thorac Surg 2010, 90(3):788-794. 10.1016/j.athoracsur.2010.04.008, 20732497.
3. Yamagami T, Yoshimatsu R, Matsumoto T, Anzai H, Yoshizawa M, Fukui Y, Nishimura T. Reproductive ability after uterine artery embolization in a sheep model: observation over 2 seasons. Reprod Sci 2010, 17(7):679-684. 10.1177/1933719110369010, 20445009.
4. Schmalstieg FC, Keeney SE, Rudloff HE, Palkowetz KH, Cevallos M, Zhou X, Cox RA, Hawkins HK, Traber DL, Zwischenberger JB. Arteriovenous CO2 removal improves survival compared to high frequency percussive and low tidal volume ventilation in a smoke/burn sheep acute respiratory distress syndrome model. Ann Surg 2007, 246(3):512-21. discussion 521-3, 10.1097/SLA.0b013e318148c6e6, 1959342, 17717455.
5. Zhou X, Wang D, Ballard-Croft CK, Simon SR, Lee HM, Zwischenberger JB. A tetracycline analog improves acute respiratory distress syndrome survival in an ovine model. Ann Thorac Surg 2010, 90(2):419-426. 10.1016/j.athoracsur.2010.04.052, 20667323.
6. Sturmer KM, Schuchardt W. [New aspects of closed intramedullary nailing and marrow cavity reaming in animal experiments. I. The tibia of the sheep, as a model for intramedullar nailing (author's transl)]. Unfallheilkunde 1980, 83(7):341-5.
7. Newman E, Turner AS, Wark JD. The potential of sheep for the study of osteopenia: current status and comparison with other animal models. Bone 1995, 16(4 Suppl):277S-284S.
8. den Boer FC, Patka P, Bakker FC, Wippermann BW, van Lingen A, Vink GQ, Boshuizen K, Haarman HJ. New segmental long bone defect model in sheep: quantitative analysis of healing with dual energy x-ray absorptiometry. J Orthop Res 1999, 17(5):654-660. 10.1002/jor.1100170506, 10569473.
9. Ravaglioli A, Krajewski A, Celotti GC, Piancastelli A, Bacchini B, Montanari L, Zama G, Piombi L. Mineral evolution of bone. Biomaterials 1996, 17(6):617-622. 10.1016/0142-9612(96)88712-6, 8652780.
10. Reichert JC, Saifzadeh S, Wullschleger ME, Epari DR, Schtz MA, Duda GN, Schell H, van Griensven M, Redl H, Hutmacher DW. The challenge of establishing preclinical models for segmental bone defect research. Biomaterials 2009, 30(12):2149-2163. 10.1016/j.biomaterials.2008.12.050, 19211141.
11. Epari DR, Schell H, Bail HJ, Duda GN. Instability prolongs the chondral phase during bone healing in sheep. Bone 2006, 38(6):864-870. 10.1016/j.bone.2005.10.023, 16359937.
12. Lienau J, Schmidt-Bleek K, Peters A, Haschke F, Duda GN, Perka C, Bail HJ, Schutze N, Jakob F, Schell H. Differential regulation of blood vessel formation between standard and delayed bone healing. J Orthop Res 2009, 27(9):1133-40. 10.1002/jor.20870, 19274756.
13. Lienau J, Schmidt-Bleek K, Peters A, Weber H, Bail HJ, Duda GN, Perka C, Schell H. Insight into the molecular pathophysiology of delayed bone healing in a sheep model. Tissue Eng Part A 2010, 16:191-9. 10.1089/ten.tea.2009.0187, 19678759.
14. Peters A, Schell H, Bail HJ, Hannemann M, Schumann T, Duda GN, Lienau J. Standard bone healing stages occur during delayed bone healing, albeit with a different temporal onset and spatial distribution of callus tissues. Histol Histopathol 2010, 25(9):1149-1162.
15. Lienau J, Schell H, Duda GN, Seebeck P, Muchow S, Bail HJ. Initial vascularization and tissue differentiation are influenced by fixation stability. J Orthop Res 2005, 23(3):639-45. 10.1016/j.orthres.2004.09.006, 15885486.
16. Schell H, Epari DR, Kassi JP, Bragulla H, Bail HJ, Duda GN. The course of bone healing is influenced by the initial shear fixation stability. J Orthop Res 2005, 23(5):1022-8. 10.1016/j.orthres.2005.03.005, 15878254.
17. Schell H, Thompson MS, Bail HJ, Hoffmann JE, Schill A, Duda GN, Lienau J. Mechanical induction of critically delayed bone healing in sheep: radiological and biomechanical results. J Biomech 2008, 41(14):3066-72. 10.1016/j.jbiomech.2008.06.038, 18778822.
18. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26(10):1135-1145. 10.1038/nbt1486, 18846087.
19. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
20. Wetterbom A, Ameur A, Feuk L, Gyllensten U, Cavelier L. Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing. Genome Biol 2010, 11(7):R78. 10.1186/gb-2010-11-7-r78, 2926789, 20653958.
21. Costa V, Angelini C, Feis ID, Ciccodicola A. Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010, 2010:853916. 2896904, 20625424.
22. Cirulli ET, Singh A, Shianna KV, Ge D, Smith JP, Maia JM, Heinzen EL, Goedert JJ, Goldstein DB, . Center for HIV/AIDS Vaccine Immunology (CHAVI) Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol 2010, 11(5):R57. 2898068, 20598109, Center for HIV/AIDS Vaccine Immunology (CHAVI).
23. Birzele F, Schaub J, Rust W, Clemens C, Baum P, Kaufmann H, Weith A, Schulz TW, Hildebrandt T. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Res 2010, 38:3999-4010. 10.1093/nar/gkq116, 2896516, 20194116.
24. Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EMK, Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010, 11:262. 10.1186/1471-2164-11-262, 2873478, 20416102.
25. Hecht J, Kuhl H, Haas SA, Bauer S, Poustka AJ, Lienau J, Schell H, Stiege AC, Seitz V, Reinhardt R, Duda GN, Mundlos S, Robinson PN. Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep. BMC Genomics 2006, 7:172. 10.1186/1471-2164-7-172, 1578570, 16822315.
26. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010, 38(6):1767-1771. 10.1093/nar/gkp1137, 2847217, 20015970.
27. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2010, (38 Database):D5-16. 10.1093/nar/gkp967, 2808881, 19910364.
28. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18(5):821-829. 10.1101/gr.074492.107, 2336801, 18349386.
29. Schulz M, Zerbino D. Oases - De novo transcriptome assembler for very short reads. Tech. rep., MPI for Molecular Genomics, European Bioinformatics Institute (EMBL-EBI), UC Santa Cruz 2010,
30. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
31. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997, 7(10):986-995.
32. Tino P. Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays. BMC Bioinformatics 2009, 10:310. 10.1186/1471-2105-10-310, 2761412, 19775462.
33. Bauer S, Gagneur J, Robinson PN. GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res 2010, 38:3523-3532. 10.1093/nar/gkq045, 2887944, 20172960.
34. Kinner B, Gerstenfeld LC, Einhorn TA, Spector M. Expression of smooth muscle actin in connective tissue cells participating in fracture healing in a murine model. Bone 2002, 30(5):738-745. 10.1016/S8756-3282(02)00695-6, 11996913.
35. Schmidt-Bleek K, Schell H, Kolar P, Pfaff M, Perka C, Buttgereit F, Duda G, Lienau J. Cellular composition of the initial fracture hematoma compared to a muscle hematoma: a study in sheep. J Orthop Res 2009, 27(9):1147-1151. 10.1002/jor.20901, 19382195.
36. Kolar P, Schmidt-Bleek K, Schell H, Gaber T, Toben D, Schmidmaier G, Perka C, Buttgereit F, Duda GN. The Early Fracture Hematoma and Its Potential Role in Fracture Healing. Tissue Eng Part B Rev 2010, 16:427-434. 10.1089/ten.teb.2009.0687, 20196645.
37. Shapiro F. Bone development and its relation to fracture repair. The role of mesenchymal osteoblasts and surface osteoblasts. Eur Cell Mater 2008, 15:53-76.
38. Le AX, Miclau T, Hu D, Helms JA. Molecular aspects of healing in stabilized and non-stabilized fractures. J Orthop Res 2001, 19:78-84. 10.1016/S0736-0266(00)00006-1, 11332624.
39. Meyer J R A, Meyer MH, Tenholder M, Wondracek S, Wasserman R, Garges P. Gene expression in older rats with delayed union of femoral fractures. J Bone Joint Surg Am 2003, 85-A(7):1243-54.
40. Niikura T, Hak DJ, Reddi AH. Global gene profiling reveals a downregulation of BMP gene expression in experimental atrophic nonunions compared to standard healing fractures. J Orthop Res 2006, 24(7):1463-71. 10.1002/jor.20182, 16705710.
41. Dalrymple BP, Kirkness EF, Nefedov M, McWilliam S, Ratnakumar A, Barris W, Zhao S, Shetty J, Maddox JF, O'Grady M, Nicholas F, Crawford AM, Smith T, de Jong PJ, McEwan J, Oddy VH, Cockett NE, . Consortium ISG Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biol 2007, 8(7):R152. 10.1186/gb-2007-8-7-r152, 2323240, 17663790, Consortium ISG.
42. Livestock Genomics. , http://www.livestockgenomics.csiro.au/sheep/
43. International Sheep Genomics Consortium. , http://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ACIV01
44. Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, Maddox JF, McEwan JC, Hutton Oddy V, Raadsma HW, Wade C, Wang J, Wang W, Xun X. The International Sheep Genomics Consortium The sheep genome reference sequence: a work in progress. Anim Genet 2010, 41(5):449-453. 10.1111/j.1365-2052.2010.02100.x, 20809919, The International Sheep Genomics Consortium.
45. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
46. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
47. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart-biological queries made easy. BMC Genomics 2009, 10:22. 10.1186/1471-2164-10-22, 2649164, 19144180.
48. Bauer S, Grossmann S, Vingron M, Robinson PN. Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 2008, 24(14):1650-1651. 10.1093/bioinformatics/btn250, 18511468.
49. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
50. Ott CE, Bauer S, Manke T, Ahrens S, Rödelsperger C, Grünhagen J, Kornak U, Duda G, Mundlos S, Robinson PN. Promiscuous and depolarization-induced immediate-early response genes are induced by mechanical strain of osteoblasts. J Bone Miner Res 2009, 24(7):1247-1262. 10.1359/jbmr.090206, 19257815.