Transcriptome sequencing and development of an expression microarray platform for the domestic ferret

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Bruder, Carl E ^a   Yao, Suxia ^a   Larson, Francis ^b   Camp, Jeremy V ^a   Tapp, Ronald ^a   McBrayer, Alexis ^a   Powers, Nicholas ^a   Valdivia Granda, Willy ^b   Jonsson, Colleen B ^a,c  

^a SOUTHERN RESEARCH INSTITUTE   (United States)

^b Orion Integrated Biosciences Inc   (United States)

^c UNIVERSITY OF LOUISVILLE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME; ALPHA GLOBIN; BETA GLOBIN;

ARTICLE; BLOOD; BRAIN; CONTROLLED STUDY; DNA MICROARRAY; DOMESTIC ANIMAL; EXPRESSED SEQUENCE TAG; FEMALE; FERRET; GENBANK; GENE EXPRESSION; GENE SEQUENCE; HOUSEKEEPING GENE; LIVER; LUNG; MALE; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; SPLEEN; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; NUCLEIC ACID DATABASE;

ANIMALIA; MUSTELA; MUSTELA PUTORIUS FURO;

ALPHA-GLOBINS; ANIMALS; BETA-GLOBINS; DATABASES, NUCLEIC ACID; EXPRESSED SEQUENCE TAGS; FERRETS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 77950951360     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-251     Document Type: Article

References (33)

1. Chu YK, Ali GD, Jia F, Li Q, Kelvin D, Couch RC, Harrod KS, Hutt JA, Cameron C, Weiss SR, Jonsson CB. The SARS-CoV ferret model in an infection-challenge study. Virology 2008, 374(1):151-163. 10.1016/j.virol.2007.12.032, 2831213, 18234270.
2. Larin NM. Canine distemper virus in the ferret. J Comp Pathol 1955, 65(4):325-333.
3. Lipatov AS, Kwon YK, Pantin-Jackwood MJ, Swayne DE. Pathogenesis of H5N1 influenza virus infections in mice and ferret models differs according to respiratory tract or digestive system exposure. J Infect Dis 2009, 199(5):717-725. 10.1086/596740, 19210164.
4. Kirkeby S, Martel CJ, Aasted B. Infection with human H1N1 influenza virus affects the expression of sialic acids of metaplastic mucous cells in the ferret airways. Virus Res 2009,
5. Maher JA, DeStefano J. The ferret: an animal model to study influenza virus. Lab Anim (NY) 2004, 33(9):50-53. 10.1038/laban1004-50, 15457202.
6. Matsuoka Y, Lamirande EW, Subbarao K. The ferret model for influenza. Curr Protoc Microbiol 2009, Chapter 15(Unit 15G):12.
7. Reuman PD, Keely S, Schiff GM. Assessment of signs of influenza illness in the ferret model. J Virol Methods 1989, 24(1-2):27-34. 10.1016/0166-0934(89)90004-9, 2760163.
8. Yen HL, Lipatov AS, Ilyushina NA, Govorkova EA, Franks J, Yilmaz N, Douglas A, Hay A, Krauss S, Rehg JE, Hoffmann E, Webster RG. Inefficient transmission of H5N1 influenza viruses in a ferret contact model. J Virol 2007, 81(13):6890-6898. 10.1128/JVI.00170-07, 1933302, 17459930.
9. Laan JW, Herberts C, Lambkin-Williams R, Boyers A, Mann AJ, Oxford J. Animal models in influenza vaccine testing. Expert Rev Vaccines 2008, 7(6):783-793. 10.1586/14760584.7.6.783, 18665776.
10. Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Paabo S. Analysis of one million base pairs of Neanderthal DNA. Nature 2006, 444(7117):330-336. 10.1038/nature05336, 17108958.
11. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
12. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452(7189):872-876. 10.1038/nature06884, 18421352.
13. Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 2007, 17(1):69-73. 10.1101/gr.5145806, 1716268, 17095711.
14. Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics 2009, 10:219. 10.1186/1471-2164-10-219, 2689275, 19435504.
15. Monaghan JR, Epp LG, Putta S, Page RB, Walker JA, Beachy CK, Zhu W, Pao GM, Verma IM, Hunter T, Bryant SV, Gardiner DM, Harkins TT, Voss SR. Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration. BMC Biol 2009, 7:1. 10.1186/1741-7007-7-1, 2630914, 19144100.
16. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17(7):1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
17. Fredericksen BL, Keller BC, Fornek J, Katze MG, Gale M. Establishment and maintenance of the innate antiviral response to West Nile Virus involves both RIG-I and MDA5 signaling through IPS-1. J Virol 2008, 82(2):609-616. 10.1128/JVI.01305-07, 2224571, 17977974.
18. Cameron MJ, Ran L, Xu L, Danesh A, Bermejo-Martin JF, Cameron CM, Muller MP, Gold WL, Richardson SE, Poutanen SM, Willey BM, DeVries ME, Fang Y, Seneviratne C, Bosinger SE, Persad D, Wilkinson P, Greller LD, Somogyi R, Humar A, Keshavjee S, Louie M, Loeb MB, Brunton J, McGeer AJ, Kelvin DJ. Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome. J Virol 2007, 81(16):8692-8706. 10.1128/JVI.00527-07, 1951379, 17537853.
19. Cameron CM, Cameron MJ, Bermejo-Martin JF, Ran L, Xu L, Turner PV, Ran R, Danesh A, Fang Y, Chan PK, Mytle N, Sullivan TJ, Collins TL, Johnson MG, Medina JC, Rowe T, Kelvin DJ. Gene expression analysis of host innate immune responses during Lethal H5N1 infection in ferrets. J Virol 2008, 82(22):11308-11317. 10.1128/JVI.00691-08, 2573250, 18684821.
20. Ramilo O, Allman W, Chung W, Mejias A, Ardura M, Glaser C, Wittkowski KM, Piqueras B, Banchereau J, Palucka AK, Chaussabel D. Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 2007, 109(5):2066-2077. 10.1182/blood-2006-02-002477, 1801073, 17105821.
21. Kobasa D, Jones SM, Shinya K, Kash JC, Copps J, Ebihara H, Hatta Y, Kim JH, Halfmann P, Hatta M, Feldmann F, Alimonti JB, Fernando L, Li Y, Katze MG, Feldmann H, Kawaoka Y. Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 2007, 445(7125):319-323. 10.1038/nature05495, 17230189.
22. Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B, Kennedy K, Wu H, Bennouna S, Oluoch H, Miller J, Vencio RZ, Mulligan M, Aderem A, Ahmed R, Pulendran B. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 2009, 10(1):116-125. 10.1038/ni.1688, 19029902.
23. Bar-Or C, Czosnek H, Koltai H. Cross-species microarray hybridizations: a developing tool for studying species diversity. Trends Genet 2007, 23(4):200-207. 10.1016/j.tig.2007.02.003, 17313995.
24. Eisenberg E, Levanon EY. Human housekeeping genes are compact. Trends Genet 2003, 19(7):362-365. 10.1016/S0168-9525(03)00140-9, 12850439.
25. Govorkova EA, Rehg JE, Krauss S, Yen HL, Guan Y, Peiris M, Nguyen TD, Hanh TH, Puthavathana P, Long HT, Buranathai C, Lim W, Webster RG, Hoffmann E. Lethality to ferrets of H5N1 influenza viruses isolated from humans and poultry in 2004. J Virol 2005, 79(4):2191-2198. 10.1128/JVI.79.4.2191-2198.2005, 546577, 15681421.
26. von Messling V, Springfeld C, Devaux P, Cattaneo R. A ferret model of canine distemper virus virulence and immunosuppression. J Virol 2003, 77(23):12579-12591. 10.1128/JVI.77.23.12579-12591.2003, 262577, 14610181.
27. Nemelka KW, Brown AW, Wallace SM, Jones E, Asher LV, Pattarini D, Applebee L, Gilliland TC, Guerry P, Baqar S. Immune response to and histopathology of Campylobacter jejuni infection in ferrets (Mustela putorius furo). Comp Med 2009, 59(4):363-371. 2779212, 19712577.
28. Maelicke A, Hoeffle-Maas A, Ludwig J, Maus A, Samochocki M, Jordis U, Koepke AK. Memogain is a Galantamine Pro-drug having Dramatically Reduced Adverse Effects and Enhanced Efficacy. J Mol Neurosci 2009,
29. Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jorgensen TE, Emblem A, Breines R, Nordeide JT, Moum T, Nederbragt AJ, Stenseth NC, Jakobsen KS. Large-scale sequence analyses of Atlantic cod. N Biotechnol 2009, 25(5):263-271. 10.1016/j.nbt.2009.03.014, 19491044.
30. Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008, 9:312. 10.1186/1471-2164-9-312, 2483731, 18590545.
31. Kawasaki H, Crowley JC, Livesey FJ, Katz LC. Molecular organization of the ferret visual thalamus. J Neurosci 2004, 24(44):9962-9970. 10.1523/JNEUROSCI.2165-04.2004, 15525781.
32. Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C. Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem 2002, 309(2):293-300. 10.1016/S0003-2697(02)00311-1, 12413463.
33. Huang X, Madan A. CAP3: A DNA sequence assembly program. Genome Res 1999, 9(9):868-877. 10.1101/gr.9.9.868, 310812, 10508846.