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Do-it-yourself: construction of a custom cDNA macroarray platform with high sensitivity and linear range

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Abstract
Background: Research involving gene expression profiling and clinical applications, such as diagnostics and prognostics, often require a DNA array platform that is flexibly customisable and cost-effective, but at the same time is highly sensitive and capable of accurately and reproducibly quantifying the transcriptional expression of a vast number of genes over the whole transcriptome dynamic range using low amounts of RNA sample. Hereto, a set of easy-to-implement practical optimisations to the design of cDNA-based nylon macroarrays as well as sample (33)P-labeling, hybridisation protocols and phosphor screen image processing were analysed for macroarray performance. Results: The here proposed custom macroarray platform had an absolute sensitivity as low as 50,000 transcripts and a linear range of over 5 log-orders. Its quality of identifying differentially expressed genes was at least comparable to commercially available microchips. Interestingly, the quantitative accuracy was found to correlate significantly with corresponding reversed transcriptase - quantitative PCR values, the gold standard gene expression measure (Pearson's correlation test p < 0.0001). Furthermore, the assay has low cost and input RNA requirements (0.5 mu g and less) and has a sound reproducibility. Conclusions: Results presented here, demonstrate for the first time that self-made cDNA-based nylon macroarrays can produce highly reliable gene expression data with high sensitivity and covering the entire mammalian dynamic range of mRNA abundances. Starting off from minimal amounts of unamplified total RNA per sample, a reasonable amount of samples can be assayed simultaneously for the quantitative expression of hundreds of genes in an easily customisable and cost-effective manner.
Keywords
CONTROL MAQC PROJECT, GENE-EXPRESSION, RNA AMPLIFICATION, MICROARRAY, PERFORMANCE, MOUSE

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Chicago
Boonefaes, Tom, Erica Houthuys, Rafael Van den Bergh, Seppe Vander Beken, Geert Raes, Peter Brouckaert, P De Baetselier, and Johan Grooten. 2011. “Do-it-yourself: Construction of a Custom cDNA Macroarray Platform with High Sensitivity and Linear Range.” Bmc Biotechnology 11.
APA
Boonefaes, T., Houthuys, E., Van den Bergh, R., Vander Beken, S., Raes, G., Brouckaert, P., De Baetselier, P., et al. (2011). Do-it-yourself: construction of a custom cDNA macroarray platform with high sensitivity and linear range. BMC BIOTECHNOLOGY, 11.
Vancouver
1.
Boonefaes T, Houthuys E, Van den Bergh R, Vander Beken S, Raes G, Brouckaert P, et al. Do-it-yourself: construction of a custom cDNA macroarray platform with high sensitivity and linear range. BMC BIOTECHNOLOGY. 2011;11.
MLA
Boonefaes, Tom, Erica Houthuys, Rafael Van den Bergh, et al. “Do-it-yourself: Construction of a Custom cDNA Macroarray Platform with High Sensitivity and Linear Range.” BMC BIOTECHNOLOGY 11 (2011): n. pag. Print.
@article{1963732,
  abstract     = {Background: Research involving gene expression profiling and clinical applications, such as diagnostics and prognostics, often require a DNA array platform that is flexibly customisable and cost-effective, but at the same time is highly sensitive and capable of accurately and reproducibly quantifying the transcriptional expression of a vast number of genes over the whole transcriptome dynamic range using low amounts of RNA sample. Hereto, a set of easy-to-implement practical optimisations to the design of cDNA-based nylon macroarrays as well as sample (33)P-labeling, hybridisation protocols and phosphor screen image processing were analysed for macroarray performance.
Results: The here proposed custom macroarray platform had an absolute sensitivity as low as 50,000 transcripts and a linear range of over 5 log-orders. Its quality of identifying differentially expressed genes was at least comparable to commercially available microchips. Interestingly, the quantitative accuracy was found to correlate significantly with corresponding reversed transcriptase - quantitative PCR values, the gold standard gene expression measure (Pearson's correlation test p {\textlangle} 0.0001). Furthermore, the assay has low cost and input RNA requirements (0.5 mu g and less) and has a sound reproducibility.
Conclusions: Results presented here, demonstrate for the first time that self-made cDNA-based nylon macroarrays can produce highly reliable gene expression data with high sensitivity and covering the entire mammalian dynamic range of mRNA abundances. Starting off from minimal amounts of unamplified total RNA per sample, a reasonable amount of samples can be assayed simultaneously for the quantitative expression of hundreds of genes in an easily customisable and cost-effective manner.},
  articleno    = {97},
  author       = {Boonefaes, Tom and Houthuys, Erica and Van den Bergh, Rafael and Vander Beken, Seppe and Raes, Geert and Brouckaert, Peter and De Baetselier, P and Grooten, Johan},
  issn         = {1472-6750},
  journal      = {BMC BIOTECHNOLOGY},
  keyword      = {CONTROL MAQC PROJECT,GENE-EXPRESSION,RNA AMPLIFICATION,MICROARRAY,PERFORMANCE,MOUSE},
  language     = {eng},
  pages        = {12},
  title        = {Do-it-yourself: construction of a custom cDNA macroarray platform with high sensitivity and linear range},
  url          = {http://dx.doi.org/10.1186/1472-6750-11-97},
  volume       = {11},
  year         = {2011},
}

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