How Gene Microarrays Work & How Our Program Saves You Time & Money
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Our microarray reader leasing program includes the following benefits:
- Leasing reduces the upfront cost of buying equipment and allows you to make payments over time
- Payments may be 100% tax-deductible*, which yields you additional savings
- Instrument downtime is eliminated with our comprehensive repair coverage
- We handle the admin work associated with equipment purchasing and maintenance
- With the cash saved through our program, companies are better able to reinvest in their core business and operations (staffing, inventory, marketing/sales, etc.)
*Please consult your tax advisor to determine the full tax implications of leasing equipment.
A DNA microarray, also commonly known as a DNA chip or biochip, is a collection of microscopic DNA spots attached to a solid surface. 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 of a specific DNA sequence, known as probes, 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 sample, or target, under high stringency conditions. This type of sample is also referred to as antisense RNA. Probe-target hybridization is usually detected and quantified by the detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine the relative abundance of nucleic acid sequences in the target.
Detection & Types
The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences specifically pairing with each other by forming hydrogen bonds between complementary nucleotide base pairs. A high number of complementary base pairs in a nucleotide sequence means tighter non-covalent bonding between the two strands. After washing off non-specific binding sequences, only strongly paired strands will remain hybridized. Fluorescently labeled target sequences that bind to a probe sequence generate a signal that depends on the hybridization conditions, such as temperature, and washing after hybridization. The total strength of the signal, from a spot (feature), depends upon the amount of target sample binding to the probes present on that spot. 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.
Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:
- The traditional solid-phase array is a collection of orderly microscopic “spots”, called features, each with thousands of identical and specific probes attached to a solid surface, such as glass, plastic or silicon biochip (commonly known as a genome chip, DNA chip or gene array). Thousands of these features can be placed in known locations on a single DNA microarray.
- The alternative bead array is a collection of microscopic polystyrene beads, each with a specific probe and a ratio of two or more dyes, which do not interfere with the fluorescent dyes used on the target sequence.
DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.
- Gene expression profiling
- Comparative genomic hybridization
- Chromatin immunoprecipitation
- SNP detection
- Alternative splicing detection
- Fusion genes microarray
- Tiling array
- Double-stranded B-DNA microarrays
- Double-stranded Z-DNA microarrays
- Multi-stranded DNA microarrays.
Microarrays can be manufactured in different ways, depending on the number of probes under examination, costs, and customization requirements, as well as the type of scientific question being asked. Arrays may have as few as 10 probes or up to 2.1 million micrometer-scale probes from commercial vendors.
Spotted vs. in situ Synthesized Arrays
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Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing, or electrochemistry on microelectrode arrays.
In spotted microarrays, the probes are oligonucleotides, cDNA, or small fragments of PCR products that correspond to mRNAs. The probes are synthesized prior to deposition on the array surface and are then “spotted” onto glass. 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 read the arrays with their own microarray scanner.
In oligonucleotide microarrays, the probes are short sequences designed to match parts of the sequence of known or predicted open reading frames. Although oligonucleotide probes are often used in “spotted” microarrays, the term “oligonucleotide array” most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by synthesizing this sequence directly onto the array surface instead of depositing intact sequences.
Two-Channel vs. One-Channel Detection
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Two-color microarrays or two-channel microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores. Fluorescent dyes commonly used for cDNA labeling include Cy3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with a laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes.
In single-channel microarrays or one-color microarrays, the arrays provide intensity data for each probe or probe set indicating a relative level of hybridization with the labeled target. However, they do not truly indicate abundance levels of a gene but rather relative abundance when compared to other samples or conditions when processed in the same experiment. Each RNA molecule encounters protocol and batch-specific bias during amplification, labeling, and hybridization phases of the experiment making comparisons between genes for the same microarray uninformative. The comparison of two conditions for the same gene requires two separate single-dye hybridizations.
If you’re interested in a microarray scanner leaseback or want to finance an automated DNA and RNA purification instrument, we can help you. Contact us at (510) 982-6552 or complete our contact form and we can discuss in more detail your specific leasing requirements.
We Provide a Wide Variety of DNA Microarray Reader Leases
This off-balance sheet financing structure provides three options at the end of the term. The lessee has the option to return the equipment to the lessor, renew at a discounted rate, or purchase the instrument for the fair market value. Monthly payments are also 100% tax deductible which yields additional monetary savings.
If you recently bought equipment, Excedr can offer you cash for your device and convert your purchase into a long-term rental. This is called a sale-leaseback. If you’ve paid for equipment within the last ninety days, we can help you recoup your investment and allow you to make low monthly payments. This also frees up money in your budget rather than tying it down to a fixed asset.
Microarray Scanner Manufacturers and Models on the Market
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GenePix, GenePix 4300A, GenePix 4400A, GenePix 4000B, GenePix 4100A
GeneChip Scanner 3000 7G System, GeneChip Scanner 3000 7G Whole-Genome Association System, GeneChip Scanner 3000 TG System, GeneChip System 3000Dx v.2, GeneTitan Multi-Channel (MC) Instrument, GeneChip miRNA 4.0 Assay, GeneChip Hybridization Oven,GeneChip Fluidics Station 450
NextSeq 550 System, iScan System
SureScan DX Microarray Scanner, SureScan Microarray Scanner
Vidia, Crocodile miniWorkstation
InnoScan 710, InnoScan 710-IR, InnoSCan 710-R, InnoScan 710-G, InnoScan 910, InnoScan 1100
ArrayPix Microplate Microarray Scanner, SpotLight CCD Microarray Scanner, Spotware Colorimetric Scanner 110, Arrayit InnoScan 1100, Arrayit InnoScan 910AL, Arrayit InnoScan 710IRAL, Arrayit InnoScan 910 Two-Color, Arrayit InnoScan 710AL, SpotLight Turbo, Arrayit InnoScan 710IR, SpotLight Blue, SpotLight
ScanRI MDx Scanner
Bio-Plex 3D Suspension Array System