Editing DNA microarray (section)

===A typical protocol===
[[File:Summary of RNA Microarray.svg|thumb|''Examples of levels of application of microarrays.'' Within the organisms, genes are transcribed and spliced to produce mature mRNA transcripts (red). The mRNA is extracted from the organism and reverse transcriptase is used to copy the mRNA into stable ds-cDNA (blue). In microarrays, the ds-cDNA is fragmented and fluorescently labelled (orange). The labelled fragments bind to an ordered array of complementary oligonucleotides, and [[Fluorometer|measurement of fluorescent intensity]] across the array indicates the abundance of a predetermined set of sequences. These sequences are typically specifically chosen to report on genes of interest within the organism's genome.<ref>{{Cite journal|last1=Shafee|first1=Thomas|last2=Lowe|first2=Rohan|date=2017|title=Eukaryotic and prokaryotic gene structure|journal=WikiJournal of Medicine|language=en|volume=4|issue=1|doi=10.15347/wjm/2017.002|issn=2002-4436|doi-access=free|s2cid=35766676 }}</ref>]]

This is an example of a '''DNA microarray experiment''' which includes details for a particular case to better explain DNA microarray experiments, while listing modifications for RNA or other alternative experiments.

# The two samples to be compared (pairwise comparison) are grown/acquired. In this example treated sample ([[Case-control|case]]) and untreated sample ([[Case-control|control]]).
# The [[nucleic acid]] of interest is purified: this can be [[RNA]] for [[expression profiling]], [[DNA]] for [[comparative hybridization]], or DNA/RNA bound to a particular [[protein]] which is [[Chromatin immunoprecipitation|immunoprecipitated]] ([[ChIP-on-chip]]) for [[Epigenetics|epigenetic]] or regulation studies. In this example total RNA is isolated (both nuclear and [[cytoplasm]]ic) by [[guanidinium thiocyanate-phenol-chloroform extraction]] (e.g. [[Trizol]]) which isolates most RNA (whereas column methods have a cut off of 200 nucleotides) and if done correctly has a better purity.
# The purified RNA is analysed for quality (by [[capillary electrophoresis]]) and quantity (for example, by using a [[NanoDrop]] or NanoPhotometer [[spectrometer]]). If the material is of acceptable quality and sufficient quantity is present (e.g., >1[[μg]], although the required amount varies by microarray platform), the experiment can proceed.
# The labeled product is generated via [[reverse transcription]] and followed by an optional [[Polymerase chain reaction|PCR]] amplification. The RNA is reverse transcribed with either polyT primers (which amplify only [[mRNA]]) or random primers (which amplify all RNA, most of which is [[rRNA]]). [[MicroRNA|miRNA]] microarrays ligate an oligonucleotide to the purified small RNA (isolated with a fractionator), which is then reverse transcribed and amplified.
#* The label is added either during the reverse transcription step, or following amplification if it is performed. The [[Sense (molecular biology)|sense]] labeling is dependent on the microarray; e.g. if the label is added with the RT mix, the [[cDNA]] is antisense and the microarray probe is sense, except in the case of negative controls.
#* The label is typically [[fluorescent]]; only one machine uses [[radioactivity in biology|radiolabels]].
#* The labeling can be direct (not used) or indirect (requires a coupling stage). For two-channel arrays, the coupling stage occurs before hybridization, using [[aminoallyl]] [[uridine]] [[triphosphate]] (aminoallyl-UTP, or aaUTP) and [[N-hydroxysuccinimide|NHS]] amino-reactive dyes (such as [[cyanine|cyanine dyes]]); for single-channel arrays, the coupling stage occurs after hybridization, using [[Biotin#Use in biotechnology|biotin]] and labeled [[Streptavidin#Uses in biotechnology|streptavidin]]. The modified nucleotides (usually in a ratio of 1 aaUTP: 4 TTP ([[thymidine triphosphate]])) are added enzymatically in a low ratio to normal nucleotides, typically resulting in 1 every 60 bases. The aaDNA is then purified with a [[DNA separation by silica adsorption|column]] (using a phosphate buffer solution, as [[Tris]] contains amine groups). The aminoallyl group is an amine group on a long linker attached to the nucleobase, which reacts with a reactive dye.
#** A form of replicate known as a dye flip can be performed to control for dye [[Artifact (error)|artifact]]s in two-channel experiments; for a dye flip, a second slide is used, with the labels swapped (the sample that was labeled with Cy3 in the first slide is labeled with Cy5, and vice versa). In this example, [[aminoallyl]]-UTP is present in the reverse-transcribed mixture.
# The labeled samples are then mixed with a proprietary [[nucleic acid hybridization|hybridization]] solution which can consist of [[Sodium dodecyl sulfate|SDS]], [[citrate|SSC]], [[dextran|dextran sulfate]], a blocking agent (such as [[Comparative genomic hybridization#Blocking|Cot-1 DNA]], salmon sperm DNA, calf thymus DNA, [[PolyA]], or PolyT), [[Denhardt's solution]], or [[Methylamine|formamine]].
# The mixture is denatured and added to the pinholes of the microarray. The holes are sealed and the microarray hybridized, either in a hyb oven, where the microarray is mixed by rotation, or in a mixer, where the microarray is mixed by alternating pressure at the pinholes.
# After an overnight hybridization, all nonspecific binding is washed off (SDS and SSC).
# The microarray is dried and scanned by a machine that uses a laser to excite the dye and measures the emission levels with a detector.
# The image is gridded with a template and the intensities of each feature (composed of several pixels) is quantified.
# The raw data is normalized; the simplest normalization method is to subtract background intensity and scale so that the total intensities of the features of the two channels are equal, or to use the intensity of a reference gene to calculate the [[t-value]] for all of the intensities. More sophisticated methods include [[z-score|z-ratio]], [[local regression|loess and lowess regression]] and RMA (robust multichip analysis) for Affymetrix chips (single-channel, silicon chip, ''in situ'' synthesized short oligonucleotides).