DNA microarrays: Difference between revisions
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DNA microarrays are used in functional genomics to determine the differences in gene expression levels between a sample and control cell<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The sample cell can be from a different tissue, at a different stage of development, at a different stage of the cell cycle, or be under different conditions (for example, exposure to a toxin)<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The DNA microarray consists of a flat surface to which oligonucleotides are bound<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. These oligonucleotides are complementary to specific cDNA sequences<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The mRNA molecules within the sample and the control are converted into labelled cDNA molecules with the use of reverse transcriptase and fluorescently-labelled nucleotides<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. For example, the cDNA of the sample can have a red fluorescence label whereas the cDNA of the control can have a green fluorescence label<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The DNA microarray is exposed to the cDNA mixture and unbound cDNA is washed away<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The resultant DNA microarray consists of spots of colour that is imaged using a confocal fluorescence scanner<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The colour of the spot is indicative of the differences in gene expression between the sample and control<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular gene compared to the control; a green spot indicates that the sample is underexpressing that particular gene compared to the control; and a yellow spot indicates that there is equal gene expression in the sample and control<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. However, the range of colours is not as discrete as suggested here but is more of a spectrum covering intermediate differences in gene expression<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. DNA microarrays are not so useful in determining gene function but can ascertain which genes may have the same regulatory mechanisms<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. | DNA microarrays are used in [[functional genomics]] to determine the differences in [[gene expression]] levels between a sample and control cell<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The sample cell can be from a different tissue, at a different stage of development, at a different stage of the cell cycle, or be under different conditions (for example, exposure to a [[toxin]])<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The DNA microarray consists of a flat surface to which [[oligonucleotides]] are bound<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. These [[oligonucleotides]] are complementary to specific [[cDNA]] sequences<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The [[mRNA]] molecules within the sample and the control are converted into labelled [[cDNA]] molecules with the use of [[reverse transcriptase]] and fluorescently-labelled [[nucleotides]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. For example, the [[cDNA]] of the sample can have a red fluorescence label whereas the [[cDNA]] of the control can have a green fluorescence label<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The DNA microarray is exposed to the [[cDNA]] mixture and unbound [[cDNA]] is washed away<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The resultant DNA microarray consists of spots of colour that is imaged using a [[confocal fluorescence scanner]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The colour of the spot is indicative of the differences in [[gene expression]] between the sample and control<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular [[gene]] compared to the control; a green spot indicates that the sample is underexpressing that particular [[gene]] compared to the control; and a yellow spot indicates that there is equal [[gene expression]] in the sample and control<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. However, the range of colours is not as discrete as suggested here but is more of a spectrum covering intermediate differences in [[gene expression]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. DNA microarrays are not so useful in determining [[gene]] function but can ascertain which genes may have the same regulatory mechanisms<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. | ||
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Revision as of 18:51, 13 November 2011
DNA microarrays are used in functional genomics to determine the differences in gene expression levels between a sample and control cell[1]. The sample cell can be from a different tissue, at a different stage of development, at a different stage of the cell cycle, or be under different conditions (for example, exposure to a toxin)[1]. The DNA microarray consists of a flat surface to which oligonucleotides are bound[1]. These oligonucleotides are complementary to specific cDNA sequences[1]. The mRNA molecules within the sample and the control are converted into labelled cDNA molecules with the use of reverse transcriptase and fluorescently-labelled nucleotides[1]. For example, the cDNA of the sample can have a red fluorescence label whereas the cDNA of the control can have a green fluorescence label[1]. The DNA microarray is exposed to the cDNA mixture and unbound cDNA is washed away[1]. The resultant DNA microarray consists of spots of colour that is imaged using a confocal fluorescence scanner[1]. The colour of the spot is indicative of the differences in gene expression between the sample and control[1]. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular gene compared to the control; a green spot indicates that the sample is underexpressing that particular gene compared to the control; and a yellow spot indicates that there is equal gene expression in the sample and control[1]. However, the range of colours is not as discrete as suggested here but is more of a spectrum covering intermediate differences in gene expression[1]. DNA microarrays are not so useful in determining gene function but can ascertain which genes may have the same regulatory mechanisms[1].