A rapid and inexpensive labeling method for microarray gene expression analysis.

BMC Biotechnology
Mario OuelletAindrila Mukhopadhyay

Abstract

Global gene expression profiling by DNA microarrays is an invaluable tool in biological research. However, existing labeling methods are time consuming and costly and therefore often limit the scale of microarray experiments and sample throughput. Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray platform with two other widely-used labeling methods, namely the NimbleGen-recommended double-stranded cDNA protocol and the indirect (aminoallyl) method. Two total RNA samples were labeled with each method and hybridized to NimbleGen expression arrays. Although all methods tested here provided similar global results and biological conclusions, the new direct random-primed cDNA labeling method provided slightly better correlation between replicates compared to the other methods and thus increased ability to find statistically significant differentially expressed genes. The new direct random-primed cDNA labeling method introduced here is suitable for gene expression microarrays and provides a rapid, inexpensive alternative to existing methods. Using NimbleGen microarrays, the method p...Continue Reading

References

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Citations

May 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jane I KhudyakovMichael P Thelen
May 11, 2010·Journal of Bacteriology·Stefan P W de VriesHester J Bootsma
Jul 2, 2014·PloS One·Marijke FrederixAindrila Mukhopadhyay
Oct 3, 2012·Metabolic Engineering·Fuzhong ZhangJay D Keasling
Feb 20, 2016·Bioconjugate Chemistry·Nicole KretschyMark M Somoza
Nov 15, 2011·The Journal of Molecular Diagnostics : JMD·John S KaddisTimothy J Triche
Nov 20, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Mathias ZaunschirmVeronika Somoza
Oct 12, 2018·Scientific Reports·Kathrin HölzMark M Somoza
Aug 20, 2019·Life Sciences in Space Research·Kianoosh PeyvanAndrew Pohorille

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Datasets Mentioned

BETA
GSE15816

Methods Mentioned

BETA
PCR

Software Mentioned

LinRegPCR
NanoStrings nCounter
nCounter
NimbleScan
VectorNTi
ArrayStar

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