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The information presented on this page will enable researchers to compare microarray platforms for Gene Expression, ChIP-on-Chip, DNA methylation, miRNA profiling, and array CGH. The goal is to assist researchers in choosing the platform that meets their needs. When selecting a platform, a number of factors should be considered including the amount of starting material required (and whether or not amplification methods are available), the array species available, the number of probes on each array and the cost of each array.

Below, we have outlined various qualities through comparison charts that may be useful if you are trying to decide which platform is best for your specific uses.

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Comparison of Gene Expression platforms (Affymetrix, Agilent, Illumina, NimbleGen, UHNMAC arrays)

	Affymetrix	Agilent	Illumina	NimbleGen	UHNMAC arrays
Amount of total RNA requested for UHNMAC service	100 ng	2 µg	200 ng	10 µg	10 µg
Is sample amplification involved in labelling the amount of RNA listed above?	Yes	Yes	Yes	No	No
What is the minimum amount of RNA required for more sensitive amplification prior to labelling?	500 pg (Using Affymetrix amplification assay; requires high quality RNA)	50 ng (Using Agilent kit)	100 pg (using second party kit)	100 pg (using second party kit)	20 pg (using Iscove amplification method)
Is there a labelling protocol specifically for FFPE or partially degraded samples?	Yes (minimum of 50ng required if RIN value is 0-4)	Yes	Yes	No	No
One- or two-colour?	one	both	one	both	both
Probe size	25-mer	60-mer	50-mer	60-mer	mostly 100-1200 bp
Species for which cataloge arrays are available   Note: custom printing is available on all platforms	Human Mouse Yeast Rat Arabidopsis Drosophila C. elegans Zebrafish & many others   Affy is the only platform to offer catalogue grape, soybean & citrus arrays	Human Mouse Yeast Rat Arabidopsis Drosophila C. elegans Zebrafish & many others   Agilent is the only platform to offer catalogue brassica, salmon & tobacco arrays	Human Mouse	Human Mouse Yeast Rat Arabidopsis Drosophila C. elegans Zebrafish & others   Prokaryotic designs covering over 200 organisms	Human Mouse Yeast
Number of probes	millions of features (over 5.3 million on Human Exon 1.0ST array)	15K, 44K, 2x105K, 244K, 1M formats available	up to 48K (Human whole genome array)	385K, HD2 (2.1 million), 4x72K, 12x135K	up to 27K features (H19K and H8K arrays face-to-face)
Analysis software typically used	GeneSpring, BioConductor	GeneSpring	Genome Studio	ArrayStar	R package,TIGR, MIDAS, MEv

Various amplification methods have been evaluated on certain different platforms. If you are using small samples, please contact us about the amplification methods that are available to you and how much total RNA is required. Also, some amplification methods require very high quality RNA samples (as determined by Agilent Bioanalyzer) while other amplification methods are more ideal for partially degraded or FFPE samples.

Comparison of ChIP-on-Chip platforms (Affymetrix, Agilent, NimbleGen, UHNMAC arrays)

	Affymetrix	Agilent	NimbleGen	UHNMAC CGI arrays
Amount of total RNA requested for UHNMAC service	9 µg PCR amplified	4 µg PCR amplified	2.5 µg(385K array) 6.5 µg(HD2 array)	10 µg PCR amplified
Probe size	25-mer	60-mer	50-75-mer	mostly 100-1200 bp
Species for which cataloge arrays are available   Note: custom printing is available on all platforms	Human Mouse Yeast Arabidopsis Drosophila C. elegans Promoter-specific Chromosome 21/22 ENCODE	Human Mouse Yeast Arabidopsis Drosophila C. elegans CpG islands Promoter-specific ENCODE	Human Mouse Rat Drosophila C. elegans	Human Mouse
Array formats	more than 6 million features possible	2x244K Custom (15K, 105K, 244K)	HD2, 385K	Human CGI 8.1K, 12K Mouse CGI 4.6K

Comparison of DNA methylation platforms (Agilent, Illumina, NimbleGen, UHNMAC arrays)

	Agilent	Illumina	NimbleGen	UHNMAC CGI arrays
Amount of DNA requested for UHNMAC service	2 µg PCR amplified or genomic DNA	1 µg genomic DNA	1 µg PCR amplified or genomic DNA	5 µg PCR amplified
Probe size	60-mer	50-mer	50-75-mer	mostly 100-1200 bp
Species for which cataloge arrays are available   Note: custom printing is available on all platforms	Human Mouse	Human	Human Mouse Rat Arabidopsis Dog Chicken	Human Mouse
Array formats	2x244K Custom (15K, 105K, 244K)	HumanMethylation27K (Infinium platform)	HD2, 385K	Human CGI 8.1K, 12K Mouse CGI 4.6K

Comparison of miRNA platforms (Affymetrix, Agilent, Illumina)

	Affymetrix	Agilent	Illumina
Amount of DNA requested for UHNMAC service	please inquire	100 ng total RNA	200 ng total RNA
1- or 2-colour	one-colour	one-colour	one-colour
Probe size	25-mer	60-mer	50-mer
Species for which cataloge arrays are available	Human Mouse Rat Canine Monkey *all species are represented on one array	Human Mouse Rat Custom printing	Human Mouse Custom printing
Array formats	mini-array (format 400) 4 identical sense probes for each miRNA	8x15K	12-sample BeadChip

Comparison of aCGH platforms (Agilent, NimbleGen)

	Agilent	NimbleGen
Amount of DNA requested for UHNMAC service	3 µg	1-5 µg (depends on array format)
Amount of DNA required for amplification	100 ng	please inquire
Probe size	60-mer	50-75-mer
Species for which cataloge arrays are available   *Custom printing is available on both platforms	Human Mouse Rat	Human Mouse Rat Drosophila C. elegans S. cerevisiae S. pombe Zebrafish Chicken Cow P. falciparum 3D7
Array formats	244K, 2x105K, 4x44K	Human: 2.1M, 385K, 12x35K, 4x72K   Mouse & others: mostly 385K format

Advantages & disadvantages of cDNA arrays (in general)

Advantages of cDNA arrays	Potential disadvantages of cDNA arrays
Increased detection sensitivity due to longer sequences	Cross-hybridisation can be a problem
Affordable (production cost is lower than for oligonucleotide arrays)	Maintaining clones and PCR amplification is labour-intensive (but this is not a problem if you are purchasing printed arrays)
Allows representation of entire genome on one array
No prior knowledge of gene expression required (use of clone library); no probe design involved

Advantages & disadvantages of oligonucleotide arrays (in general)

Advantages of oligo arrays	Potential disadvantages of oligo arrays
Higher specificity (less cross-hybrisation due to shorter probes)	Decreased sensitivity due to shorter sequences (lower sensitivity compensated by use of multiple probes)
More uniform melting temperatures	Expensive to design and manufacture
Detection of SNP and splice variants	Prior knowledge of sequence required
Higher uniformity of spots (controlled amount of material per spot)

Comparison of Affymetrix and Agilent oligonucleotide arrays (in general)

Affymetrix arrays	Agilent arrays
Only one-colour system is offered	Both one- and two-colour systems One-colour allows for experimental design to change throughout project; good for projects that will take place over a long period of time with an initially unknown number of samples Two-colour is a more direct comparison of two samples
Decreased sensitivity due to shorter 25-mer sequences; however, lower sensitivity compensated by fact that multiple oligos represent each gene	Longer 60-mers are more tolerant of sequence mismatches and thus are more suitable for analysis of highly polymorphic regions
Additional equipment required (specialised fluidics station and Affymetrix-specific scanner)