Editing Transcriptome (section)

=== DNA microarrays ===
{{main|DNA microarray}}
[[File:Affymetrix-microarray.jpg|thumb|[[DNA microarray]] used to detect gene expression in human (''left'') and mouse (''right'') samples]]

The first transcriptome studies were based on [[microarray]] techniques (also known as DNA chips). Microarrays consist of thin glass layers with spots on which [[oligonucleotide]]s, known as "probes" are arrayed; each spot contains a known DNA sequence.<ref>{{Cite journal|title=Quantitative monitoring of gene expression patterns with a complementary DNA microarray|last1=Schena|first1=M.|last2=Shalon|first2=D.|date=20 October 1995|journal=Science|location=New York, N.Y. |volume=270|number=5235|pages=467–470|issn=0036-8075|pmid=7569999|last3=Davis|first3=R. W.|last4=Brown|first4=P. O.|doi = 10.1126/science.270.5235.467|bibcode = 1995Sci...270..467S|s2cid=6720459}}</ref>

When performing microarray analyses, mRNA is collected from a control and an experimental sample, the latter usually representative of a disease. The RNA of interest is converted to cDNA to increase its stability and marked with [[fluorophore]]s of two colors, usually green and red, for the two groups. The cDNA is spread onto the surface of the microarray where it hybridizes with oligonucleotides on the chip and a laser is used to scan. The fluorescence intensity on each spot of the microarray corresponds to the level of gene expression and based on the color of the fluorophores selected, it can be determined which of the samples exhibits higher levels of the mRNA of interest.<ref name="microarrays" />

One microarray usually contains enough oligonucleotides to represent all known genes; however, data obtained using microarrays does not provide information about unknown genes. During the 2010s, microarrays were almost completely replaced by next-generation techniques that are based on DNA sequencing.