Measuring microRNAs: Comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods

BMC Biotechnology

Volumn 8, Issue , 2008, Pages

  Ach, Robert A ^a   Wang, Hui ^a   Curry, Bo ^a  

^a AGILENT LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION METHODS; COSMIC RAYS; HISTOLOGY; MICROARRAYS; NUCLEIC ACIDS; RNA; SENSITIVITY ANALYSIS;

AGILENT; ANALYSIS METHODS; CELLULAR REGULATION; DIFFERENTIAL SENSITIVITY; EXPRESSION LEVELS; HUMAN TISSUES; MICRO-RNAS; MICROARRAY ANALYSIS; QUANTITATIVE PCR; QUANTITATIVE RT-PCR; SAMPLE PREPARATION METHODS; STARTING MATERIALS;

BIOASSAY;

2 PROPANOL; GUANIDINE; MICRORNA; PHENOL;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; COMPARATIVE STUDY; DNA MICROARRAY; GENETICS; LABORATORY DIAGNOSIS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS;

BASE SEQUENCE; MICRORNAS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, RNA; SPECIMEN HANDLING;

EID: 52449110023     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-8-69     Document Type: Article

References (38)

1. Nilsen TW Mechanisms of microRNA-mediated gene regulation in animal cells Trends Genet 2007, 23:243-249 10.1016/j.tig.2007.02.011 17368621
2. Pillai RS Bhattacharyya SN Filipowicz W Repression of protein synthesis by miRNAs: How many mechanisms? Trends Cell Biol 2007, 17:118-126 10.1016/j.tcb.2006.12.007 17197185
3. Eulalio A Huntzinger E Izaurralde E Getting to the root of miRNA-mediated gene silencing Cell 2007, 132:9-14 10.1016/ j.cell.2007.12.024
4. Vasudevan S Tong Y Steitz J Switching from repression to activation: MicroRNAs can up-regulate translation Science 2008, 318:1931-1934 10.1126/science.1149460
5. Leung AKL Sharp PA microRNAs: A safeguard against turmoil? Cell 2007, 130:581-585 10.1016/j.cell.2007.08.010 17719533
6. Ambros V The functions of animal microRNAs Nature 2004, 431:350-355 10.1038/nature02871 15372042
7. Kloosterman WP Plasterk RH The diverse functions of microRNAs in animal development and disease Dev Cell 2006, 11:441-450 10.1016/ j.devcel.2006.09.009 17011485
8. Calin GA Croce CM MicroRNA signatures in human cancers Nat Rev Cancer 2006, 6:857-866 10.1038/nrc1997 17060945
9. Garzon R Fabbr M Cimmino A Calin GA Croce CM MicroRNA expression and function in cancer Trends Mol Med 2006, 12:580-587 10.1016/ j.molmed.2006.10.006 17071139
10. Griffiths-Jones S Grocock RJ van Dongen S Bateman A Enright AJ miRBase: microRNA sequences, targets and gene nomenclature Nuc Acids Res 2006, 34:D140-D144 10.1093/nar/gkj112
11. Griffiths-Jones S The microRNA registry Nuc Acids Res 2004, 32:D109-D111 10.1093/nar/gkh023
12. The miRBase Database http://microrna.sanger.ac.uk
13. Bentwich I Avniel A Karov Y Aharonov R Gilad S Barad O Barzilai A Einat P Einav U Meiri E Sharon E Spector Y Bentwich Z Identification of hundreds of conserved and nonconserved human microRNAs Nat Genet 2005, 37:766-770 10.1038/ng1590 15965474
14. Miranda KC Huynh T Tay Y Ang Y-S Tam W-L Thomson AM Lim B Rigoutsos I A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes Cell 2006, 126:1203-1217 10.1016/ j.cell.2006.07.031 16990141
15. Chen C Ridzon DA Broomer AJ Zhou Z Lee DH Nguyen JT Barbisin M Xu NL Mahuvakar VR Andersen MR Lao KQ Livak KJ Guegler KJ Real-time quantification of microRNAs by stem-loop RT-PCR Nuc Acids Res 2005, 33:e179 10.1093/nar/gni178
16. Liang Y Ridzon D Wong L Chen C Characterization of microRNA expression profiles in normal human tissues BMC Genomics 2007, 8:166 1904203 17565689 10.1186/1471-2164-8-166
17. Raymond CJ Roberts BS Garrett-Engele P Lim LP Johnson JM Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs RNA 2005, 11:1737-1744 1370860 16244135 10.1261/rna.2148705
18. Stratagene http://www.stratagene.com/products/displayProduct.aspx?pid=820
19. QIAGEN http://www1.qiagen.com/products/miRNA/miScriptSystem.aspx
20. Landgraf P Rusu M Sheridan R Sewer A Iovino N Aravin A Pfeffer S Rice A Kamphorst AO Landthaler M Lin C Socci ND Hermida L Fulci V Chiaretti S Foa R Schliwka J Fuchs U Novosel A Muller R-U Schermer B Bissels U Inman J Phan Q Chien M Weir DB Choksi R De Vita G Frezzeti D Trompeter H-I Hornung V Teng G Hartmann G Palkovits M Di Lauro R Wernet P Macino G Rogler CE Nagle JW Ju J Papavasiliou FN Benzing T Lichter P Tam W Brownstein MJ Bosio A Borkhardt A Russo JJ Sander C Zavolan M Tuschl T A mammalian microRNA expression atlas based on small library sequencing Cell 2007, 129:1401-1414 10.1016/j.cell.2007.04.040 17604727
21. Mattie MD Benz CC Bowers J Sensinger K Wong L Scott GK Fedele V Ginzinger D Getts R Haqq C Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies Mol Cancer 2006, 5:24 1563474 16784538 10.1186/ 1476-4598-5-24
22. Bloomston M Frankel WL Petrocca F Volinia S Alder H Hagan JP Liu C-G Bhatt D Taccioli C Croce CM MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis JAMA 2007, 297:1901-1908 10.1001/jama.297.17.1901 17473300
23. Porkka KP Pfeiffer MJ Waltering KK Vessella RL Tammela TLJ Visakorpi T MicroRNA expression profiling in prostate cancer Cancer Res 2007, 67:6130-6135 10.1158/0008-5472.CAN-07-0533 17616669
24. Calin GA Liu C-G Sevignani C Ferracin M Felli N Dumitru CD Shimizu M Cimmino A Zupo S Dono M Dell'Aquila ML Alder H Rassenti L Kipps TJ Bullrich F Negrini M Croce CM MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias Proc Natl Acad Sci USA 2004, 101:11755-11760 511048 15284443 10.1073/pnas.0404432101
25. Volinia S Calin GA Liu C-G Ambs S Cimmino A Petrocca F Visone R Iorio M Roldo C Ferracin M Prueitt RL Yanaihara N Lanza G Scarpa A Vecchione A Negrini M Harris CC Croce CM A microRNA expression signature of human solid tumors defines cancer gene targets Proc Natl Acad Sci USA 2006, 103:2257-2261 1413718 16461460 10.1073/pnas.0510565103
26. Wang H Ach RA Curry B Direct and sensitive miRNA profiling from low-input total RNA RNA 2007, 13:151-159 1705746 17105992 10.1261/ rna.234507
27. Calin GA Liu C-G Sevignani C Ferracin M Felli N Dumitru CD Shimizu M Cimmino A Zupo S Dono M Dell'Aquila ML Alder H Rassenti L Kipps TJ Bullrich F Negrini M Croce C MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias Proc Natl Acad Sci USA 2004, 101:11755-11760 511048 15284443 10.1073/pnas.0404432101
28. Beuvink I Kolb FA Budach W Garnier A Lange J Natt F Dengler U Hall J Filipowicz W Weiler J A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs Nuc Acids Res 2007, 35:e52 10.1093/nar/gkl1118
29. Saba R Booth SA Target labeling for the detection and profiling of microRNAs expressed in CNS tissues using microarrays BMC Biotechnol 2006, 6:47 1713234 17164008 10.1186/1472-6750-6-47
30. Wu H Neilson JR Kumar P Manocha M Shankar P Sharp PA Manjunath N miRNA profiling of naive, effector and memory CD8 T cells PLoS ONE 2007, 2:e1020 2000354 17925868 10.1371/journal.pone.0001020
31. Agilent Technologies http://www.opengenomics.com/webcastinfo.aspx?wid=36
32. Agilent Technologies http://www.opengenomics.com/webcastinfo.aspx?wid=28
33. Enos JM Duzeski JL Roesch PL Hagstrom JE Watt M-AV MicroRNA labeling methods directly influence the accuracy of expression profiling detection BioTechniques 2007, 42:378-381 10.2144/000112448
34. van Rooij E Sutherland LB Qi X Richardson JA Hill J Olson EN Control of stress-dependent cardiac growth and gene expression by a microRNA Science 2007, 316:575-579 10.1126/science.1139089 17379774
35. Schroeder A Mueller O Stocker S Salowsky R Leiber M Gassmann M Lightfoot S Menzel W Granzow M Ragg T The RIN: An RNA integrity number for assigning integrity values to RNA measurements BMC Mol Biol 2006, 7:3 1413964 16448564 10.1186/1471-2199-7-3
36. Imbeaud S Graudens E Boulanger V Barlet X Zaborski P Eveno E Mueller O Schroeder A Auffray C Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces Nuc Acids Res 2005, 33:e56 10.1093/nar/gni054
37. Agilent Technologies http://www.chem.agilent.com/scripts/PHome.asp
38. Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE11879