DiscovArray™ Probes / ContentRNA DNA Asuragen


The MOST CONTENT Available On Any Platform

The DiscovArray miRNA Expression Service, utilizing the Ambion miRChip V1, offers the most content available on any miRNA profiling platform, allowing you to interrogate a dramatically larger number of putative miRNAs.


Validated and exploratory content totaling > 13,000 candidate miRNAs from various sources.†

In addition to Sanger content, other sources of candidate miRNAs have been included to discover novel expression patterns.


Ambion miRChip V1
miRNA Content
Human
Rat
Mouse
Sanger miRBase V9.2
475 probes
234 probes
377 probes
DiscovArray content
467 probes
234 probes
293 probes
DiscovArray % of Sanger V9.2
98.3%
100.0%
77.7%
Exploratory content
12,894 probes
Homology likely
Total probes
13,349 probes

Comparison to Sanger 10.0 Content


The following table offers both a conservative (left panels) and liberal (right panels) comparison of the Ambion miRChip V1 content to the Sanger 10.0 miRBase.


Ambion miRChip V1 content
Perfect match to unique Sanger microRNA sequences1 Candidates likely to measure signal from a Sanger miRNA/precursors2
Species miRChip V1 Sanger 10.0 coverage
miRChip V1
Sanger 10.0
coverage
Anopheles gambiae
35
37
 94.6% 38 38 100.0%
Apis mellifera
37
51
 72.5% 42 54 77.8%
Arabidopsis thaliana
71
154
 46.1% 117 184 63.6%
Ateles geoffroyi
42
42
 100.0% 45 45 100.0%
Bombyx mori
19
21
 90.5% 19 21 90.5%
Bos taurus
115
125
 92.0% 112 117 95.7%
Brassica napus
5
5
 100.0% 5 5 100.0%
Caenorhabditis briggsae
76
92
 82.6% 79 95 83.2%
Caenorhabditis elegans
113
136
 83.1% 113 135 83.7%
Canis familiaris
5
5
 100.0% 6 6 100.0%
Chlamydomonas reinhardtii
0
84
 0.0% 0 49 0.0%
Cricetulus griseus
1
1
 100.0% 1 1 100.0%
Danio rerio
180
219
 82.2% 315 337 93.5%
Drosophila melanogaster
72
93
 77.4% 78 93 83.9%
Drosophila pseudoobscura
62
68
 91.2% 73 73 100.0%
Epstein Barr virus
6
39
 15.4% 5 23 21.7%
Fugu rubripes
108
109
 99.1% 131 131 100.0%
Gallus gallus
126
131
 96.2% 147 149 98.7%
Glycine max
15
15
 100.0% 22 22 100.0%
Gorilla gorilla
81
81
 100.0% 86 86 100.0%
Herpes Simplex Virus 1
0
2
 0.0% 0 2 0.0%
Homo sapiens
616
711
 86.6% 486 533 91.2%
Human cytomegalovirus
14
17
 82.4% 11 11 100.0%
Human immunodeficiency virus 1
0
2
 0.0% 0 2 0.0%
Kaposi sarcoma-associated herpesvirus
16
17
 94.1% 12 13 92.3%
Lagothrix lagotricha
45
45
 100.0% 48 48 100.0%
Lemur catta
15
15
 100.0% 16 16 100.0%
Macaca mulatta
70
70
 100.0% 71 71 100.0%
Macaca nemestrina
71
71
 100.0% 75 75 100.0%
Mareks disease virus
0
10
 0.0% 0 8 0.0%
Mareks disease virus type 2
0
27
 0.0% 0 17 0.0%
Medicago truncatula
14
17
 82.4% 29 30 96.7%
Monodelphis domestica
91
99
 91.9% 103 107 96.3%
Mouse gammaherpesvirus 68
8
10
 80.0% 9 9 100.0%
Mus musculus
360
568
 63.4% 323 442 73.1%
Oryza sativa
92
115
 80.0% 178 243 73.3%
Ovis aries
4
4
 100.0% 4 4 100.0%
Pan paniscus
84
84
 100.0% 89 89 100.0%
Pan troglodytes
78
80
 97.5% 82 83 98.8%
Physcomitrella patens
14
187
 7.5% 51 220 23.2%
Pinus taeda
5
23
 21.7% 9 27 33.3%
Pongo pygmaeus
81
81
 100.0% 84 84 100.0%
Populus trichocarpa
99
100
 99.0% 215 215 100.0%
Rattus norvegicus
291
348
 83.6% 256 285 89.8%
Rhesus lymphocryptovirus
0
22
 0.0% 1 16 6.2%
Rhesus monkey rhadinovirus
0
11
 0.0% 0 7 0.0%
Saccharum officinarum
10
10
 100.0% 16 16 100.0%
Saguinus labiatus
40
40
 100.0% 42 42 100.0%
Schmidtea mediterranea
1
73
 1.4% 4 63 6.3%
Selaginella moellendorffii
5
60
 8.3% 14 58 24.1%
Simian virus 40
2
2
 100.0% 1 1 100.0%
Sorghum bicolor
39
39
 100.0% 72 72 100.0%
Sus scrofa
52
52
 100.0% 54 54 100.0%
Tetraodon nigroviridis
108
109
 99.1% 132 132 100.0%
Triticum aestivum
8
31
 25.8% 9 32 28.1%
Xenopus laevis
7
7
 100.0% 7 7 100.0%
Xenopus tropicalis
126
159
 79.2% 156 177 88.1%
Zea mays
43
43
 100.0% 96 96 100.0%
Total Coverage
3678
4869
 75.5% 4189 5071 82.6%

1. Perfect match to unique Sanger microRNA sequences
The values reported as “Sanger 10.0” in this case are the number of unique mature miRNA sequences annotated in the Sanger miRBase for each organism.  The values shown under "miRChip V1" are the number of these sequence-unique mature miRNAs that are probed by at least one miRChip V1 probe with a 100% perfect match.  Therefore it reflects the most conservative number of Sanger mature miRNA, and the most conservative estimate of unique probes to these miRNA.

2. Candidates likely to measure signal from a Sanger miRNA/precursors
The values reported as "Sanger 10.0" in this case are the number of unique precursors annotated in the Sanger miRBase for each organism, regardless of whether a mature miRNA appears on multiple precursors.  The values reported as "miRChip V1" are the number of these named unique precursors for which at least one probe on the miRChip V1 has at least 90% overlap with no internal mismatches.  This table demonstrates what the miRChip is likely to detect based on the commonly referenced number of miRNAs in the Sanger miRBase.

Stay ahead of Sanger miRBase with a single chip
 
Profile your samples today using content which is likely to be in future releases of Sanger miRBase. Annotation files will be updated with each Sanger update to facilitate analysis of historical data sets relative to the latest Sanger annotations.
 
Open the window to exploratory content
 

The addition of exploratory content allows you to find novel miRNA expression patterns in specific tissues or disease states. An internal survey of ten normal human tissues compared the number of Sanger miRNAs detected to the number of exploratory miRNA seqences detected. A 28% detection rate for predicted human miRNAs was obtained using the DiscovArray Service.




Ambion miRChip V1 Oligo Probe Design

miRNAs are a highly evolutionarily conserved class of small non-coding RNAs that are recently found to be negative regulators of gene expression. The length of mature miRNAs range between 18 and 25 nucleotides (nt). The short minimal sequence available for hybridization and wide range of melting temperatures of miRNA sequences pose serious challenges for miRNA array design.
 
The design of the Ambion miRNA miRChip V1 was based on Affymetrix GeneChip platform. The comprehensive content of 13,349 unique known and predicted miRNA mature sequences were selected from miRBase release 8.2 and other sources †. Unique mature miRNA sequences were defined as having at least one nucleotide base difference in pair wise comparison.

Two overlapping probes were designed for each mature miRNA candidate.  The staggered probe design provides the flexibility required for probes to capture slight variations in the ends of the processed mature miRNA. For computationally predicted miRNA, this probe design strategy accounts for the uncertainty associated with predicting the precise cleavage site of the processed mature miRNA.


Interested in Asuragen's other miRNA services? [Click here]

†References:

1. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: miRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 2006, 34, D140-D144.
2. Cummins, Proc Natl Acad Sci USA 103(10):3687-92, 2006);
3. Xie, Nature 434(7031):338-45, 2005);
4. Berezikov, Cell 120(1):21-4, 2005);
5. Bentwich, Nat Genet. 2005 Jul;37(7):766-70 (method for miRNA predictions).