Evaluation of procedures for amplification of small-size samples for hybridization on microarrays

被引:59
作者
Klur, S
Toy, K
Williams, MP
Certa, U [1 ]
机构
[1] F Hoffmann La Roche & Co Ltd, Roche Ctr Med Genom, CH-4070 Basel, Switzerland
[2] Genentech Inc, Dept Mol Biol, San Francisco, CA 94080 USA
关键词
gene expression profiling; oligonucleotide microarrays; laser capture microdissection; RNA amplification techniques;
D O I
10.1016/j.ygeno.2003.09.005
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Various approaches have been developed for the preparation of samples for gene expression monitoring. For Affymetrix chips, a standard protocol is widely used; however, this is inefficient for small samples such as laser capture microdissections. Several amplification procedures for such samples already exist, and our goal was to test two of them: the first is based on random PCR amplification, and the second, linear amplification, involves performing the standard protocol twice. We analyzed a dilution of a commercially available mouse brain total RNA preparation and microdissections from mouse hippocampus and striatum. We evaluated the quality of microarray data by analyzing several chip parameters and performing multiple comparisons. At the biological level, brain microdissections prepared with either method gave similar expression results. At the technical level, analysis of the commercial sample showed that random PCR amplification is more reproducible, requires smaller RNA input, and generates cRNA of higher quality than linear amplification. (C) 2003 Elsevier Inc. All rights reserved.
引用
收藏
页码:508 / 517
页数:10
相关论文
共 32 条
[1]   Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays [J].
Alon, U ;
Barkai, N ;
Notterman, DA ;
Gish, K ;
Ybarra, S ;
Mack, D ;
Levine, AJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (12) :6745-6750
[2]  
[Anonymous], 1993, Statistical Theory
[3]   A faithful method for PCR-mediated global mRNA amplification and its integration into microarray analysis on laser-captured cells [J].
Aoyagi, K ;
Tatsuta, T ;
Nishigaki, M ;
Akimoto, S ;
Tanabe, C ;
Omoto, Y ;
Hayashi, S ;
Sakamoto, H ;
Sakamoto, M ;
Yoshida, T ;
Terada, M ;
Sasaki, H .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2003, 300 (04) :915-920
[4]  
Bohm M, 1997, AM J PATHOL, V151, P63
[5]  
Certa U, 2001, Methods Mol Biol, V170, P141
[6]   Expression profile of 30,000 genes in rat hippocampus using SAGE [J].
Datson, NA ;
van der Perk, J ;
de Kloet, ER ;
Vreugdenhil, E .
HIPPOCAMPUS, 2001, 11 (04) :430-444
[7]   Expression profiling using cDNA microarrays [J].
Duggan, DJ ;
Bittner, M ;
Chen, YD ;
Meltzer, P ;
Trent, JM .
NATURE GENETICS, 1999, 21 (Suppl 1) :10-14
[8]   ANALYSIS OF GENE-EXPRESSION IN SINGLE LIVE NEURONS [J].
EBERWINE, J ;
YEH, H ;
MIYASHIRO, K ;
CAO, YX ;
NAIR, S ;
FINNELL, R ;
ZETTEL, M ;
COLEMAN, P .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (07) :3010-3014
[9]   Laser capture microdissection [J].
EmmertBuck, MR ;
Bonner, RF ;
Smith, PD ;
Chuaqui, RF ;
Zhuang, ZP ;
Goldstein, SR ;
Weiss, RA ;
Liotta, LA .
SCIENCE, 1996, 274 (5289) :998-1001
[10]   Advantages of mRNA amplification for microarray analysis [J].
Feldman, AL ;
Costouros, NG ;
Wang, E ;
Qian, M ;
Marincola, FM ;
Alexander, HR ;
Libutti, SK .
BIOTECHNIQUES, 2002, 33 (04) :906-+