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Array Platforms |
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Affymetrix |
cDNA |
Oligo |
Agilent Oligo |
Illumina |
| Description |
Extensive informatics intrinsic to Affymetrix
software |
Inter-experiment comparisons can be difficult,
unless done on exactly same slide print batch |
Inter-experiment comparisons can be difficult,
unless done on exactly same slide print batch |
Highest correlation between technical replicates |
Most up-to-date probe set available. Highly scalable and flexible platfrom |
| Specificity |
High (short redundant oligo probes) |
Low (due to cross hybridization) |
Average |
High |
High |
| Genes/Chip |
12,000-47,000 |
Up to 50,000 cDNA/slide (human, mouse, rat, others) |
Up to 70,000 oligos (human, mouse, rat, others) |
20,000 to 37,000 genes |
~48,000 human transcripts; ~47,000 mouse transcripts; 22,000 rat transcripts |
| Chip Sets |
47,000 human genes available on single chip; similar numbers of rodent genes available on two chips |
custom (9k mouse, 6k human) |
Operon oligo sets |
37,000 human genes on single chip; more than 20,000 mouse and rat genes/chip |
46,000 human genes available on one chip |
| Cost/Array |
$250-$450 |
$75 |
$75 |
$190-$450 |
$160-$175 |
| Labeling Costs/Array |
$150 |
$87.50 |
$87.50 |
$100 |
$40 |
| Equipment Cost |
$200,000 |
$125,000 |
$125,000 |
$130,000 |
$350,000 |
| Ease of Customization |
Low (custom chips are rare and expensive) |
High - Completely customizable (user defines
genes to be printed) |
High -Completely customizable (user defines
genes to be printed) – currently Operon oligo sets are
available in the MC |
High - Completely customizable (user defines genes to be printed) |
High- Completely costomizable (user defines genes to be printed) |
| Notes |
Little or no variation between chips allows
straightforward inter-experiment, inter-lab comparisons
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Often some “drop out” of spots due to printing process
and not all clones sequence-verified, causing tracking issues
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All oligonucleotide sequences are verified; occasional “drop out” of some spots due to printing process
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Most reproducible system
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100% quality tested and most cost effective platform. Simple protocols and requires only 50 to 100 ng of starting total RNA.
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