An optimized RNA amplification method for prokaryotic expression profiling analysis

Applied Microbiology and Biotechnology

Volumn 87, Issue 1, 2010, Pages 343-352

  Cao, Feng Lin ^a   Liu, Han Hua ^b   Wang, Ya Hui ^b   Liu, Yu ^b   Zhang, Xiao Yu ^b   Zhao, Jian Qing ^b   Sun, Yi Min ^b   Zhou, Jin ^c   Zhang, Liang ^b  

^a THE FIRST AFFILIATED HOSPITAL OF HARBIN MEDICAL UNIVERSITY   (China)

^b NATIONAL ENGINEERING RESEARCH CENTER FOR BEIJING BIOCHIP TECHNOLOGY   (China)

^c HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Microarray analysis; Prokaryotic expression; RNA amplification; Target preparation method

Indexed keywords

BACKGROUND NOISE; CONVENTIONAL METHODS; DIFFERENTIAL GENE EXPRESSIONS; DNA MICROARRAY TECHNOLOGY; E. COLI; EUKARYOTIC GENE EXPRESSION; EXPRESSION PROFILING; GENE EXPRESSION ANALYSIS; HEAT-SHOCK; IN-VITRO; MESSENGER RNAS (MRNA); MICRO-ARRAY CHIPS; MICROARRAY ANALYSIS; POLYADENYLATION; PROKARYOTIC EXPRESSION; RANDOM PRIMERS; REVERSE TRANSCRIPTION; RNA POLYMERASE; SPECIFIC PRIMERS; TARGET PREPARATION; TRANSCRIPTOMES;

AMPLIFICATION; ESCHERICHIA COLI; TARGETS; TRANSCRIPTION;

RNA;

BACTERIAL RNA;

EUKARYOTE; GENE EXPRESSION; GENETIC ENGINEERING; HYBRIDIZATION; OPTIMIZATION; PROKARYOTE; RNA; SIMULATION;

ACCURACY; ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE EXPRESSION; HUMAN; MICROARRAY ANALYSIS; POLYADENYLATION; PROKARYOTE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SENSITIVITY AND SPECIFICITY; TRANSCRIPTOMICS; EUKARYOTE; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; NUCLEIC ACID AMPLIFICATION; PROCEDURES;

ESCHERICHIA COLI; EUKARYOTA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; RNA, BACTERIAL;

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

EID: 77952889816     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-010-2459-9     Document Type: Article

References (37)

1. LR Baugh AA Hill EL Brown CP Hunter 2001 Quantitative analysis of mRNA amplification by in vitro transcription Nucleic Acids Res 29 E29 10.1093/nar/29.5.e29 1:STN:280:DC%2BD3M3jsFWmsw%3D%3D
2. AC Eklund LR Turner P Chen RV Jensen G deFeo AR Kopf-Sill Z Szallasi 2006 Replacing cRNA targets with cDNA reduces microarray cross-hybridization Nat Biotechnol 24 1071 1073 10.1038/nbt0906-1071 1:CAS:528:DC%2BD28XptlSlsrs%3D (Pubitemid 44359710)
3. P Francois C Garzoni M Bento J Schrenzel 2007 Comparison of amplification methods for transcriptomic analyses of low abundance prokaryotic RNA sources J Microbiol Methods 68 385 391 10.1016/j.mimet.2006.09.022 1:CAS:528: DC%2BD2sXhtVCgsL0%3D (Pubitemid 46157260)
4. H Gao ZK Yang TJ Gentry L Wu CW Schadt J Zhou 2007 Microarray-based analysis of microbial community RNAs by whole-community RNA amplification Appl Environ Microbiol 73 563 571 10.1128/AEM.01771-06 1:CAS:528:DC%2BD2sXhtFCqs7o%3D (Pubitemid 46147587)
5. JG Hacia 1999 Resequencing and mutational analysis using oligonucleotide microarrays Nat Genet 21 42 47 10.1038/4469 1:CAS:528:DyaK1MXltlWhtA%3D%3D (Pubitemid 29031491)
6. K Iida I Nishimura 2002 Gene expression profiling by DNA microarray technology Crit Rev Oral Biol Med 13 35 50 10.1177/154411130201300105
7. SA Jelinsky LD Samson 1999 Global response of Saccharomyces cerevisiae to an alkylating agent Proc Natl Acad Sci USA 96 1486 1491 10.1073/pnas.96.4.1486 1:CAS:528:DyaK1MXhsFSru7s%3D (Pubitemid 29098477)
8. A Kallioniemi OP Kallioniemi D Sudar D Rutovitz JW Gray F Waldman D Pinkel 1992 Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors Science 258 818 821 10.1126/science.1359641 1:CAS:528:DyaK3sXhs1Gn
9. AB Khodursky BJ Peter NR Cozzarelli D Botstein PO Brown C Yanofsky 2000 DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli Proc Natl Acad Sci USA 97 12170 12175 10.1073/pnas.220414297 1:CAS:528: DC%2BD3cXnvVSgtbg%3D
10. DL Lakey Y Zhang AM Talaat B Samten LE DesJardin KD Eisenach SA Johnston PF Barnes 2002 Priming reverse transcription with oligo(dT) does not yield representative samples of Mycobacterium tuberculosis cDNA Microbiology 148 2567 2572 1:CAS:528:DC%2BD38XmslSqtr8%3D
11. Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94(24):13057-13062
12. KS LeMessurier AD Ogunniyi JC Paton 2006 Differential expression of key pneumococcal virulence genes in vivo Microbiology 152 305 311 10.1099/mic.0.28438-0 1:CAS:528:DC%2BD28XhsVKnsLg%3D (Pubitemid 43210661)
13. T Li Y Li ZY Han Q Chen MY Qiu S Ni ZL Jiang Y Xie YM Mao 2003 Optimization of T7-based RNA amplification system for cDNA microarray Acta Bioch Bioph Sin 35 441 448 1:CAS:528:DC%2BD3sXhtVWitbjO
14. L Li J Roden BE Shapiro BJ Wold S Bhatia SJ Forman R Bhatia 2005 Reproducibility, fidelity, and discriminant validity of mRNA amplification for microarray analysis from primary hematopoietic cells J Mol Diagnostics 7 48 56 1:CAS:528:DC%2BD2MXhvFKrtrs%3D
15. E Manduchi LM Scearce JE Brestelli GR Grant KH Kaestner CJ Stoeckert Jr 2002 Comparison of different labeling methods for two-channel high-density microarray experiments Physiol Genomics 10 169 179 1:CAS:528: DC%2BD38XnvV2mt7k%3D
16. KD Meier O Deloche K Kajiwara K Funato H Riezman 2006 Sphingoid base is required for translation initiation during heat stress in Saccharomyces cerevisiae Mol Biol Cell 17 1164 1175 10.1091/mbc.E05-11-1039 1:CAS:528:DC%2BD28XltlSqt7Y%3D (Pubitemid 43376538)
17. M Moreno-Paz V Parro 2006 Amplification of low quantity bacterial RNA for microarray studies: time-course analysis of Leptospirillum ferrooxidans under nitrogen-fixing conditions Environ Microbiol 8 1064 1073 10.1111/j.1462-2920. 2006.00998.x 1:CAS:528:DC%2BD28Xmt1Srsrk%3D (Pubitemid 43901773)
18. ST Motley BJ Morrow X Liu IL Dodge A Vitiello CK Ward KJ Shaw 2004 Simultaneous analysis of host and pathogen interactions during an in vivo infection reveals local induction of host acute phase response proteins, a novel bacterial stress response, and evidence of a host-imposed metal ion limited environment Cell Microbiol 6 849 865 10.1111/j.1462-5822.2004.00407.x 1:CAS:528:DC%2BD2cXms1eiuro%3D (Pubitemid 39162627)
19. JP Muyal SK Singh H Fehrenbach 2008 DNA-microarray technology: comparison of methodological factors of recent technique towards gene expression profiling Crit Rev Biotechnol 28 239 251 10.1080/07388550802428400 1:CAS:528: DC%2BD1cXhsVGqtL7P
20. V Nygaard E Hovig 2006 Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling Nucleic Acids Res 34 996 1014 10.1093/nar/gkj499 1:CAS:528: DC%2BD28Xhs1Sku78%3D (Pubitemid 43380683)
21. CS Richmond JD Glasner R Mau HF Jin FR Blattner 1999 Genome-wide expression profiling in Escherichia coli K-12 Nucleic Acids Res 27 3821 3835 10.1093/nar/27.19.3821 1:CAS:528:DyaK1MXms1Wru74%3D (Pubitemid 29454430)
22. KH Rohde RB Abramovitch DG Russell 2007 Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues Cell Host Microbe 2 352 364 10.1016/j.chom.2007.09.006 1:CAS:528: DC%2BD2sXhtlyhtL3F (Pubitemid 350056395)
23. N Sarkar 1997 Polyadenylation of mRNA in prokaryotes Ann Rev Biophys 66 173 197 1:CAS:528:DyaK2sXktFOitbc%3D
24. R Singh RJ Maganti SV Jabba M Wang G Deng JD Heath N Kurn P Wangemann 2005 Microarray-based comparison of three amplification methods for nanogram amounts of total RNA Am J Phys 288 C1179 C1189 10.1152/ajpcell.00258.2004 1:CAS:528:DC%2BD2MXktlSgurg%3D (Pubitemid 40559393)
25. SS Sisodia B Sollner-Webb DW Cleveland 1987 Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation Mol Cell Biol 7 3602 3612 1:CAS:528: DyaL2sXlvFaiurY%3D
26. L Tailleux SJ Waddell M Pelizzola A Mortellaro M Withers A Tanne PR Castagnoli B Gicquel NG Stoker PD Butcher M Foti O Neyrolles 2008 Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages PLoS ONE 3 e1403 10.1371/journal.pone.0001403 (Pubitemid 351194013)
27. VG Tusher R Tibshirani G Chu 2001 Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci USA 98 5116 5121 10.1073/pnas.091062498 1:CAS:528:DC%2BD3MXjt1Ons7w%3D (Pubitemid 32397092)
28. DF Veiga FF Vicente M Grivet A de la Fuente AT Vasconcelos 2007 Genome-wide partial correlation analysis of Escherichia coli microarray data Genet Mol Res 6 730 742 1:CAS:528:DC%2BD2sXhtlWks7%2FK
29. R Villuendas JL Steegmann M Pollan L Tracey A Granda E Fernandez-Ruiz LF Casado J Martinez P Martinez L Lombardia L Villalon J Odriozola MA Piris 2006 Identification of genes involved in imatinib resistance in CML: a gene-expression profiling approach Leukemia 20 1047 1054 10.1038/sj.leu.2404197 1:CAS:528:DC%2BD28XkvVymtb4%3D (Pubitemid 43797296)
30. SJ Waddell K Laing C Senner PD Butcher 2008 Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies BMC Genomics 9 94 10.1186/1471-2164-9-94 (Pubitemid 351461070)
31. E Wang 2005 RNA amplification for successful gene profiling analysis J Transl Med 3 28 10.1186/1479-5876-3-28 (Pubitemid 41522079)
32. Y Wei JM Lee C Richmond FR Blattner JA Rafalski RA LaRossa 2001 High-density microarray-mediated gene expression profiling of Escherichia coli J Bacteriol 183 545 556 10.1128/JB.183.2.545-556.2001 1:CAS:528: DC%2BD3MXktVOksQ%3D%3D (Pubitemid 32048113)
33. CL Wilson SD Pepper Y Hey CJ Miller 2004 Amplification protocols introduce systematic but reproducible errors into gene expression studies BioTechniques 36 498 506 1:CAS:528:DC%2BD2cXitlertLw%3D
34. Q Xia D Cheng J Duan G Wang T Cheng X Zha C Liu P Zhao F Dai Z Zhang N He L Zhang Z Xiang 2007 Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori Genome Biol 8 R162 10.1186/gb-2007-8-8-r162 (Pubitemid 351891475)
35. CC Xiang M Chen L Ma QN Phan JM Inman OA Kozhich MJ Brownstein 2003 A new strategy to amplify degraded RNA from small tissue samples for microarray studies Nucleic Acids Res 31 e53 10.1093/nar/gng053
36. YH Yang S Dudoit P Luu DM Lin V Peng J Ngai TP Speed 2002 Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 30 e15 10.1093/nar/30.4.e15
37. H Zhao T Hastie ML Whitfield AL Borresen-Dale SS Jeffrey 2002 Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis BMC Genomics 3 31 10.1186/1471-2164-3-31 1:CAS:528:DC%2BD3sXmtFWqurk%3D (Pubitemid 39565254)