Development and validation of a bovine macrophage specific cDNA microarray

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Jensen, Kirsty ^a   Talbot, Richard ^a   Paxton, Edith ^a   Waddington, David ^a   Glass, Elizabeth J ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GAMMA INTERFERON; INTERLEUKIN 6; LIPOPOLYSACCHARIDE; PRION PROTEIN; RNA; TOLL LIKE RECEPTOR 4;

ANIMAL CELL; ARTICLE; BONE MARROW CELL; CATTLE; CELL CLONE; CONTROLLED STUDY; DNA LIBRARY; DNA MICROARRAY; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION; GENE SEQUENCE; MACROPHAGE; MALE; MONOCYTE; NONHUMAN; NUCLEOTIDE SEQUENCE; STATISTICAL SIGNIFICANCE; STIMULUS; UNINDEXED SEQUENCE; VALIDATION PROCESS;

ANIMALS; CATTLE; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; INTERFERON-GAMMA; LIPOPOLYSACCHARIDES; MACROPHAGES; MOLECULAR SEQUENCE DATA; MONOCYTES; MYELOID CELLS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ANIMALIA; BOS TAURUS;

EID: 33749428998     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-224     Document Type: Article

References (56)

1. Glass EJ, Innes EA, Spooner RL, Brown CG: Infection of bovine monocyte/ macrophage populations with Theileria annulato and Theileria parva. Vet Immunol Immunopathol 1989, 22:355-368.
2. Bogdan C, Röllinghoff M: How do protozoan parasites survive inside macrophages? Parasitol Today 1999, 15:22-28.
3. McGuire K, Glass EJ: The expanding role of microarrays in the investigation of macrophage responses to pathogens. Vet Immunol Immunopathol 2005, 105:259-275.
4. Chitko-McKown CG, Fox JM, Miller LC, Heaton MP, Bono JL, Keen JE, Grosse WM, Laegreid WW. Gene expression profiling of bovine macrophages in response to Escherichia coli 0157:H7 lipopolysaccharide. Dev Comp Immunol 2004, 28:635-645.
5. Weiss DJ, Evanson OA, Deng M, Abrahamsen MS: Gene expression and antimicrobial activity of bovine macrophages in response to Mycobacterium avium subsp. paratuberculosis. Vet Pathol 2004, 41:326-337.
6. Weiss DJ, Evanson OA, Deng MQ, Abrahamsen MS: Sequential patterns of gene expression by bovine monocyte-derived macrophages associated with ingestion of mycobacterial organisms. Microb Pathogenesis 2004, 37:215-224.
7. Werling D, Ruryk A, Heaney J, Moeller E, Brownlie J: Ability to differentiate between cp and ncp BVDV by microarrays: Towards an application in clinical veterinary medicine? Vet Immunol Immunopathol 2005, 108:157-164.
8. Wedlock DN, Kawakami RP, Koach J, Buddle BM, Collins DM: Differences of gene expression in bovine alveolar macrophages infected with virulent and attenuated isogenic strams of Mycobacterium bovis. Int Immunopharmacol 2006, 6:957-961.
9. Staudt LM, Brown PO: Genomic views of the immune system. Annu Rev Immunol 2000, 18:829-859.
10. Wells C, Ravasi T, Sultana R, Yagi K, Carninci P, Bono H, Faulkner G, Okazaki Y, Quackenbush J, Hume DA, Lyons PA: Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Res 2003, 13:1360-1365.
11. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schanbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y: Functional annotation of a full-length mouse cDNA collection. Nature 2001, 409:685-690.
12. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami & Schonbach C, Golobori T, Baldarelli R, Hill DP, Butt C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420:563-573.
13. Jensen K, Speed D, Paxton E, Williams JL, Glass EJ: Construction of a normalized Bos taurus and Bos indicus macrophage specific cDNA library. Anim Genet 2006, 37:75-77.
14. Iseli C, Jongeneel CV, Bucher P: ESTScan; a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. P Int Conf Intell Syst Mol Biol 1999:138-148.
15. ESTScan [http://www.ch.embnet.org/software/ESTScan.html]
16. Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW: Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res 2001, 11:626-630.
17. Sonstegard TS, Capuco AV, White J, Van Tassell CP, Connor EE, Cho J, Sultana R, Shade L, Wray JE, Wells KD, Quackenbush J: Analysis of bovine mammary gland EST and functional annotation of the Bos tourus gene index. Mamm Genome 2002, 13:373-379.
18. ARK-Genomics Centre for Functional Genomics in Farm Animals [http://www.ark-genomics.org]
19. Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone S: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31:68-71.
20. ArrayExpress [http://www.ebi.ac.uk/arrayexpress]
21. Tempelman RJ: Assessing statistical precision, power and robustness of alternative experimental designs for two colour microarray platforms based on mixed effects models. Vet Immunol Immunopathol 2005, 105:175-186.
22. Yao J, Burton JL, Saama P, Sipkovsky S, Coussens PM: Generation of EST and cDNA microarray resources for the study of bovine immunobiology. Acta Vet Scand 2001, 42:391-405.
23. Hill EW, O'Gorman GM, Agaba M, Gibson JP, Hanotte O, Kemp SJ, Naessens J, Coussens PM, MacHugh DE: Understanding bovine trypanosomiasis and trypanotolerance: the promise of functional genomics. Vet Immunol Immunopathol 2005, 105:247-258.
24. Tao W, Mallard BA, Karrow N, Bridle B: Construction and application of a bovine immune-endocrine cDNA microarray. Vet Immunol Immunopathol 2004, 101:1-17.
25. Donaldson L, Vuocolo T, Gray C, Strandberg Y, Reverter A, McWilliam S, Wang YH, Byrne K, Tellam R: Construction and validation of a bovine innate immune microarray. BMC Genomics 2005, 6:135.
26. Band MR, Olmstead C, Everts RE, Liu ZL, Lewin HA: A 3800 gene microarray for cattle functional genomics: comparison of gene expression in spleen, placenta, and brain. Anim Biotechnol 2002, 13:163-172.
27. Gao JJ, Diesl V, Wittmann T, Morrison DC, Ryan JL, Vogel SN, Follettie MT: Bacterial LPS and CpG DNA differentially induce gene expression profiles in mouse macrophages. J Endotoxin Res 2003, 9:237-243.
28. Nau GJ, Richmond JFL, Schlesinger A, Jennings EG, Lander ES, Young RA: Human macrophage activation programs induced by bacterial pathogens. P Natl Acad Sci USA 2002, 99:1503-1508.
29. Chaussabel D, Semnani RT, McDowell MA, Sacks D, Sher A, Nutman TB: Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. Blood 2003, 102:672-681.
30. Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, Blake J, Chan F, Gonzalez C, Zhang L, Samaha RR: Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics 2006, 7-59.
31. Evertsz EM, Au-Young J, Ruvolo MV, Lim AC, Reynolds MA: Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays. Biotechniques 2001, 31:1182-1192.
32. Patel OV, Suchyta SP, Sipkovsky SS, Yao J, Ireland JJ, Coussens PM, Smith GW: Validation and application of a high fidelity mRNA linear amplification procedure for profiling gene expression. Vet Immunol Immunopathol 2005, 105:331-342.
33. Rouzaut A, Lopez-Moratalla N, de Miguel C: Differential gene expression in the activation and maturation of human monocytes. Arch Biochem Biophys 2000, 374:153-160.
34. Zhou AQ, Herriott MJ, Leu RW: Kinetics of the biosynthesis of complement subcomponent Clq by murine macrophages: LPS, immune complexes, and zymosan alone and in combination with interferon-gamma. J Leukocyte Biol 1991, 50:453-463.
35. Dürig J, Giese A, Schulz-Schaeffer W, Rosenthal C, Schmücker U, Bieschke J, Dührsen U, Kretzschmar HA: Differential constitutive and activation-dependent expression of prion protein in human peripheral blood leucocytes. Br J Haematol 2000, 108:488-496.
36. de Almeida CJG, Chiarini LB, da Silva JP, e Silva PMR, Martins MA, Linden R: The cellular prion protein modulates phagocytosis and inflammatory response. J Leukocyte Biol 2005, 77:238-246.
37. Burthem J, Urban B, Pain A, Roberts DJ: The normal cellular prion protein is strongly expressed by myeloid dendritic cells. Blood 2001, 98:3733-3738.
38. Sun Y, Leaman DW: Involvement of noxa in cellular apoptotic responses to interferon, double-stranded RNA, and virus infection. J Biol Chem 2005, 280:15561-15568.
39. Bogerd HP, Wiegard HL, Doehle BP, Lueders KK, Cullen BR: APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposan function in human cells. Nucleic Acids Res 2006, 34:89-95.
40. Scheibenbogen C, Keiholz U, Richter M, Andreesen R, Hunstein W: The interleukin-2 receptor in human monocytes and macrophages: regulation of expression and release of the alpha and beta chains (p55 and p75). Res Immunol 1992, 143:33-37.
41. Dekkers PEP, Juffermans NP, ten Hove T, de Jonge E, van Deventer SJH, van der Poll T: Endotoxin down-regulates monocyte and granulocyte interleukin-6 receptors without influencing gp130 expression in humans. J Infect Dis 2000, 181:1055-1061.
42. Parker LC, Whyte MKB, Vogel SN, Dower SK, Sabroe I: Toll-like receptor (TLR)2 and TLR4 agonists regulate CCR expression in human monocytic cells. J Immunol 2004, 172:4977-4986.
43. Grey ST, Tsuchida A, Hau H, Orthner CL, Salem HH, Hancock WW: Selective inhibitory effects of the anticoagulant activated protein C on the responses of human mononuclear phagocytes to LPS, IFN-γ, or phorbol ester. J Immunol 1994, 153:3664-3672.
44. Pei L, Castrillo A, Chen M, Hoffmann A, Tontonoz P: Induction of NR4A orphan nuclear receptor expression in macrophages in response to inflammatory stimuli. J Biol Chem 2005, 280:29256-29262.
45. Begum NA, Kobayashi M, Moriwaki Y, Matsumoto M, Toyoshima K, Seya T: Mycobacterium bovis BCG cell wall and lipopolysaccharide induce a novel gene, BIGM103, encoding a 7-TM protein: identification of a new protein family having Zn-transporter and Zn-metalloprotease signatures. Genomics 2002, 80:630-645.
46. Rozen S, Skaletsky HJ: Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics Methods and Protocols: Methods in Molecular Biology Edited by: Krawetz S, Misener S. Totowa: Humana Press; 2000:365-386.
47. Primer3 [http://frodo.wi.mit.edu/cgi-bin/promer3/primer3_www.cgi]
48. Brooke GP, Parsons KR, Howard CJ: Cloning of two members of the SIRPα family of protein tyrosine phosphatase binding proteins in cattle that are expressed on monocytes and a sub-population of dendritic cells and which mediate binding to CD4 T cells. Eur J Immunol 1998, 28:1-11.
49. Smyth GK: Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor Edited by: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber. New York: Springer; 2005:397-420.
50. Smyth GK, Speed TP: Normalization of cDNA microarray data. Methods 2003, 31:265-273.
51. Baird D, Johnstone P, Wilson T: Normalization of microarray data using a spatial mixed model analysis which includes splines. Bioinformatics 2004, 20:3196-3205.
52. Smyth GK: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 2004, 3(1): Article 3
53. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B Met 1995, 57:289-300.
54. NetPrimer [http://www.premierbiosoft.com/netprimer/netprlaunch/ netprlaunch.html]
55. Pfaffl MW: A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids-Res 2001, 29:e45.
56. Roslin Institute [http://www.roslin.ac.uk/about/staff/ Bovine_Macrophage_cDNA_Microarray.xls]