Reading this paper they said this:
Contemporary microarrays emerged in the wake of genome sequencing projects for one obvious reason: arrays require a priori knowledge of the query genome
Why do you need a priori knowledge? Thanks.
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4$\begingroup$ How do you think people know what sequence to put on the probesets? $\endgroup$– user438383Feb 18, 2021 at 9:19
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$\begingroup$ There is a bit of ambiguity in the term of "microarrays", which is currently mostly used to relate to "microarrays" that detect nucleic acids through their sequence-mediated binding (see excellent answer below from Pascal). While much rarer, there would also be "microarrays" directed at other chemicals, such as proteins binding antibodies: en.wikipedia.org/wiki/Antibody_microarray $\endgroup$– tsttstFeb 19, 2021 at 1:37
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1 Answer
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If the query genome is unknown, a microarray cannot be made for a target species. Microarrays have DNA fragments of what you want to amplify on them. Those fragments must be known.
From nature:
DNA microarrays are microscope slides that are printed with thousands of tiny spots in defined positions, with each spot containing a known DNA sequence or gene.
From wikipedia:
Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (${10^{−12}}$ moles) of a specific DNA sequence, known as probes (or reporters or oligos). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target) under high-stringency conditions.
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1$\begingroup$ This answer consists of two quotations, neither of which is an answer to what in my opinion comes under the heading of "questions that show insuffiient thought to be worth answering". You state that "Microarrays have DNA fragments of what you want to amplify on them". This is incorrect. 1. There is no amplification "on" the fragments. — the cDNA generated from the mRNA may be regarded as amplified. 2. They are not DNA fragments. They are synthetic deoxyoligonucleotides. Please edit your answer such that it is is clear and correct. $\endgroup$– DavidFeb 18, 2021 at 21:39
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$\begingroup$ Some good clarification. Maybe @David, you might consider editing the Wikipedia article. $\endgroup$– pascalFeb 19, 2021 at 5:10