Validating microarray data
Microarrays use relative quantitation in which the intensity of a feature is compared to the intensity of the same feature under a different condition, and the identity of the feature is known by its position.
DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as c DNA after reverse transcription) that may or may not be translated into proteins.
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 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 c DNA or c RNA (also called anti-sense RNA) sample (called target) under high-stringency conditions.
The purpose is to empirically detect expression of transcripts or alternatively spliced forms which may not have been previously known or predicted.These sequences are typically specifically chosen to report on genes of interest within the organism's genome.A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface.Example protein to immunoprecipitate are histone modifications (H3K27me3, H3K4me2, H3K9me3, etc.), Polycomb-group protein (PRC2: Suz12, PRC1: YY1) and trithorax-group protein (Ash1) to study the epigenetic landscape or RNA Polymerase II to study the transcription landscape.Analogously to Ch IP, genomic regions bound by a protein of interest can be isolated and used to probe a microarray to determine binding site occupancy.
Left-handed double-stranded Z-DNA microarrays can be used to identify short sequences of the alternative Z-DNA structure located within longer stretches of right-handed B-DNA genes (e.g., transcriptional enhancement, recombination, RNA editing).