DNA microarray: Difference between revisions

Revision as of 21:39, 10 June 2022

Revision as of 18:14, 11 September 2022

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In ''spotted microarrays'', the probes are [[oligonucleotide synthesis|oligonucleotide]]s, [[cDNA]] or small fragments of [[PCR]] products that correspond to [[mRNA]]s. The probes are [[oligonucleotide synthesis|synthesized]] prior to deposition on the array surface and are then "spotted" onto glass. A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations on the array surface. The resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or cRNA "targets" derived from experimental or clinical samples.

This technique is used by research scientists around the world to produce "in-house" printed microarrays fromin their own labs. These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. This provides a relatively low-cost microarray that may be customized for each study, and avoids the costs of purchasing often more expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator.

Publications exist which indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays,<ref name="TRC Standardization">{{cite journal |date=2005 |title=Standardizing global gene expression analysis between laboratories and across platforms |journal=Nat Methods |volume=2 |pages=351–356 |pmid=15846362 |doi=10.1038/nmeth754 |last12=Deng |first12=S |last13=Dressman |first13=HK |last14=Fannin |first14=RD |last15=Farin |first15=FM |last16=Freedman |first16=JH |last17=Fry |first17=RC |last18=Harper |first18=A |last19=Humble |first19=MC |last20=Hurban |first20=P |last21=Kavanagh |first21=TJ |last22=Kaufmann |first22=WK |first23=KF |first24=L |first25=JA |first26=MR |last27=Li |first27=J |first28=YJ |last29=Lobenhofer |first29=EK |last30=Lu |last31=Malek |first31=RL |last32=Milton |first32=S |last33=Nagalla |first33=SR |last34=O'malley |first34=JP |last35=Palmer |first35=VS |last36=Pattee |first36=P |last7=Paules |first7=RS |last38=Perou |first38=CM |last9=Phillips |first39=K |last40=Qin |last41=Qiu |first41=Y |last42=Quigley |first42=SD |last43=Rodland |first43=M |last44=Rusyn |first44=I |last45=Samson |first45= LD|last46= Schwartz|last47=Shi |first47=Y |last48=Shin |last49=Sieber |last50=Slifer |last51=Speer |first51=MC |last52=Spencer |first52=PS |last53=Sproles |first53=DI |last54=Swenberg |first54=JA |last55=Suk|first55= WA |last56=Sullivan |first56=RC |last57=Tian |first57=R |last58=Tennant |first58=RW |last59= Todd |first59=SA |last60=Tucker |first60=CJ |last61=Van Houten |first61=B |last62=Weis |first62=BK |last63=Xuan |first63=S |last64=Zarbl |first64=H |last65=Members Of The Toxicogenomics Research |first65=Consortium |issue=5 |author1=Bammler T, Beyer RP |author2=Consortium, Members of the Toxicogenomics Research |last3=Kerr |last4=Jing |last5=Lapidus |last6=Lasarev |last8=Li |first3=X |first4=LX |first6=DA |first8=JL |first9=SO |first5=S |s2cid=195368323 }}</ref> possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays.