Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples

被引:144
作者
Bertucci, F
Bernard, K
Loriod, B
Chang, YC
Granjeaud, S
Birnbaum, D
Nguyen, C
Peck, K
Jordan, BR [1 ]
机构
[1] CIML Luminy, F-13288 Marseille 9, France
[2] Inst Cancerol & Immunol Marseille, TAGC, F-13288 Marseille, France
[3] Inst J Paoli I Calmettes, F-13009 Marseille, France
[4] Acad Sinica, Inst Biomed Sci, Taipei, Taiwan
关键词
D O I
10.1093/hmg/8.9.1715
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
DNA or oligonucleotide arrays are widely used for large-scale expression measurements, using various implementations: macroarrays in which DNA is spotted onto nylon membranes of relatively large dimensions (with radioactive detection) on the one hand; microarrays on glass slides and oligonucleotide chips, both used with fluorescent probes, on the other hand. Nylon microarrays with colourimetric detection have also been described recently. The small physical dimensions of miniaturized systems allow small hybridization volumes (2-100 mu l) and provide high probe concentrations, in contrast to macroarrays. We show, however, that actual sensitivity (defined as the amount of sample necessary for detection of a given mRNA species) is in fact similar for ail these systems and that this is mostly due to the very different amounts of target material present on the respective arrays. We then demonstrate that the combination of nylon microarrays with P-33-labelled radioactive probes provides 100-fold better sensitivity, making it possible to perform expression profiling experiments using submicrogram amounts of unamplified total RNA from small biological samples. This has important implications in basic and clinical research and makes this alternative approach particularly suitable for groups operating in an academic context.
引用
收藏
页码:1715 / 1722
页数:8
相关论文
共 23 条
[1]   Multiplex messenger assay: Simultaneous, quantitative measurement of expression of many genes in the context of T cell activation [J].
Bernard, K ;
Auphan, N ;
Granjeaud, S ;
Victorero, G ;
SchmittVerhulst, AM ;
Jordan, BR ;
Nguyen, C .
NUCLEIC ACIDS RESEARCH, 1996, 24 (08) :1435-1442
[2]   Expression scanning of an array of growth control genes in human tumor cell lines [J].
Bertucci, F ;
Van Hulst, S ;
Bernard, K ;
Loriod, B ;
Granjeaud, S ;
Tagett, R ;
Starkey, M ;
Nguyen, C ;
Jordan, B ;
Birnbaum, D .
ONCOGENE, 1999, 18 (26) :3905-3912
[3]   Options available - from start to finish - for obtaining expression data by microarray [J].
Bowtell, DDL .
NATURE GENETICS, 1999, 21 (Suppl 1) :25-32
[4]   Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection [J].
Chen, JJW ;
Wu, R ;
Yang, PC ;
Huang, JY ;
Sher, YP ;
Han, MH ;
Kao, WC ;
Lee, PJ ;
Chiu, TF ;
Chang, F ;
Chu, YW ;
Wu, CW ;
Peck, K .
GENOMICS, 1998, 51 (03) :313-324
[5]   The transcriptional program of sporulation in budding yeast [J].
Chu, S ;
DeRisi, J ;
Eisen, M ;
Mulholland, J ;
Botstein, D ;
Brown, PO ;
Herskowitz, I .
SCIENCE, 1998, 282 (5389) :699-705
[6]   Exploring the metabolic and genetic control of gene expression on a genomic scale [J].
DeRisi, JL ;
Iyer, VR ;
Brown, PO .
SCIENCE, 1997, 278 (5338) :680-686
[7]   From hybridization image to numerical values: A practical, high throughput quantification system for high density filter hybridizations [J].
Granjeaud, S ;
Nguyen, C ;
Rocha, D ;
Luton, R ;
Jordan, BR .
GENETIC ANALYSIS-BIOMOLECULAR ENGINEERING, 1996, 12 (3-4) :151-162
[8]   HYBRIDIZATION FINGERPRINTING OF HIGH-DENSITY CDNA-LIBRARY ARRAYS WITH CDNA POOLS DERIVED FROM WHOLE TISSUES [J].
GRESS, TM ;
HOHEISEL, JD ;
LENNON, GG ;
ZEHETNER, G ;
LEHRACH, H .
MAMMALIAN GENOME, 1992, 3 (11) :609-619
[9]   The transcriptional program in the response of human fibroblasts to serum [J].
Iyer, VR ;
Eisen, MB ;
Ross, DT ;
Schuler, G ;
Moore, T ;
Lee, JCF ;
Trent, JM ;
Staudt, LM ;
Hudson, J ;
Boguski, MS ;
Lashkari, D ;
Shalon, D ;
Botstein, D ;
Brown, PO .
SCIENCE, 1999, 283 (5398) :83-87
[10]   Large-scale expression measurement by hybridization methods: From high-density membranes to "DNA chips" [J].
Jordan, BR .
JOURNAL OF BIOCHEMISTRY, 1998, 124 (02) :251-258