DiscovArray™ Probes / Content
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.
|
DiscovArray™ Ambion miRChip V1 content
|
Human
|
Rat
|
Mouse
|
|
Sanger miRBase 11.0
|
837 probes
|
350 probes
|
599 probes
|
|
DiscovArray™ content
|
623 probes
|
292 probes
|
361 probes
|
|
DiscovArray™ % of Sanger 11.0
|
74%
|
83%
|
60%
|
|
Exploratory content
|
>12,000 probes
|
Homology likely
|
|
Total probes
|
13,349 probes
|
|
|
Comparison to Sanger 11.0 Content
The following table offers both a conservative (left panels) and liberal (right
panels) comparison of the Ambion miRChip V1 content to the Sanger 11.0 miRBase.
|
|
DiscovArray™ Ambion miRChip V1 content
|
|
|
Perfect match to unique Sanger microRNA sequences1
|
Candidates likely to measure signal from a Sanger miRNA/precursors2
|
|
Species
|
DiscovArray™
|
Sanger 11.0
|
Coverage
|
DiscovArray™
|
Sanger 11.0
|
Coverage
|
|
Anopheles gambiae
|
37
|
44
|
84%
|
40
|
45
|
89%
|
|
Apis mellifera
|
37
|
51
|
73%
|
42
|
54
|
78%
|
|
Arabidopsis thaliana
|
71
|
154
|
46%
|
117
|
184
|
64%
|
|
Ateles geoffroyi
|
42
|
54
|
78%
|
45
|
60
|
75%
|
|
Bombyx mori
|
19
|
21
|
91%
|
19
|
21
|
91%
|
|
Bos taurus
|
115
|
125
|
92%
|
112
|
117
|
96%
|
|
Brassica napus
|
17
|
24
|
71%
|
41
|
46
|
89%
|
|
Brassica oleracea
|
0
|
1
|
0%
|
0
|
0
|
0%
|
|
Brassica rapa
|
0
|
1
|
0%
|
0
|
1
|
0%
|
|
Caenorhabditis briggsae
|
76
|
92
|
83%
|
79
|
95
|
83%
|
|
Caenorhabditis elegans
|
113
|
156
|
72%
|
113
|
154
|
73%
|
|
Canis familiaris
|
151
|
177
|
85%
|
179
|
203
|
88%
|
|
Carica papaya
|
1
|
1
|
100%
|
1
|
1
|
100%
|
|
Chlamydomonas reinhardtii
|
0
|
84
|
0%
|
0
|
49
|
0%
|
|
Ciona intestinalis
|
7
|
32
|
22%
|
10
|
34
|
29%
|
|
Ciona savignyi
|
7
|
25
|
28%
|
8
|
27
|
30%
|
|
Cricetulus griseus
|
1
|
1
|
100%
|
1
|
1
|
100%
|
|
Danio rerio
|
180
|
219
|
82%
|
315
|
337
|
94%
|
|
Dictyostelium discoideum
|
0
|
2
|
0%
|
0
|
2
|
0%
|
|
Drosophila melanogaster
|
72
|
152
|
47%
|
78
|
152
|
51%
|
|
Drosophila pseudoobscura
|
62
|
68
|
91%
|
73
|
73
|
100%
|
|
Epstein Barr virus
|
6
|
39
|
15%
|
5
|
23
|
22%
|
|
Fugu rubripes
|
108
|
109
|
99%
|
131
|
131
|
100%
|
|
Gallus gallus
|
126
|
131
|
96%
|
147
|
149
|
99%
|
|
Glycine max
|
15
|
15
|
100%
|
22
|
22
|
100%
|
|
Gorilla gorilla
|
81
|
81
|
100%
|
86
|
86
|
100%
|
|
Gossypium herbecium
|
1
|
1
|
100%
|
1
|
1
|
100%
|
|
Gossypium hirsutum
|
5
|
7
|
71%
|
10
|
13
|
77%
|
|
Gossypium rammindii
|
1
|
1
|
100%
|
2
|
2
|
100%
|
|
Herpes Simplex Virus 1
|
0
|
0
|
0%
|
0
|
1
|
0%
|
|
Homo sapiens
|
623
|
837
|
74%
|
502
|
678
|
74%
|
|
Human cytomegalovirus
|
14
|
17
|
82%
|
11
|
11
|
100%
|
|
Human immunodeficiency virus 1
|
0
|
4
|
0%
|
0
|
3
|
0%
|
|
Kaposi sarcoma-associated herpesvirus
|
16
|
17
|
94%
|
12
|
13
|
92%
|
|
Lagothrix lagotricha
|
45
|
45
|
100%
|
48
|
48
|
100%
|
|
Lemur catta
|
15
|
15
|
100%
|
16
|
16
|
100%
|
|
Macaca mulatta
|
337
|
480
|
70%
|
352
|
464
|
76%
|
|
Macaca nemestrina
|
71
|
71
|
100%
|
75
|
75
|
100%
|
|
Mareks disease virus
|
0
|
22
|
0%
|
0
|
13
|
0%
|
|
Mareks disease virus type 2
|
0
|
27
|
0%
|
0
|
17
|
0%
|
|
Medicago truncatula
|
14
|
17
|
82%
|
29
|
30
|
97%
|
|
Monodelphis domestica
|
91
|
110
|
83%
|
103
|
119
|
87%
|
|
Mouse cytomegalovirus
|
0
|
29
|
0%
|
0
|
18
|
0%
|
|
Mouse gammaherpesvirus 68
|
8
|
10
|
80%
|
9
|
9
|
100%
|
|
Mus musculus
|
361
|
599
|
60%
|
324
|
472
|
69%
|
|
Oikopleura dioica
|
1
|
63
|
2%
|
6
|
66
|
9%
|
|
Oryza sativa
|
92
|
142
|
65%
|
180
|
269
|
67%
|
|
Ovis aries
|
4
|
4
|
100%
|
4
|
4
|
100%
|
|
Pan paniscus
|
84
|
84
|
100%
|
89
|
89
|
100%
|
|
Pan troglodytes
|
81
|
92
|
88%
|
91
|
100
|
91%
|
|
Physcomitrella patens
|
14
|
187
|
8%
|
51
|
220
|
23%
|
|
Pinus taeda
|
5
|
25
|
20%
|
9
|
29
|
31%
|
|
Pongo pygmaeus
|
81
|
81
|
100%
|
84
|
84
|
100%
|
|
Populus trichocarpa
|
99
|
112
|
88%
|
215
|
234
|
92%
|
|
Pygathrix bieti
|
3
|
9
|
33%
|
7
|
11
|
64%
|
|
Rattus norvegicus
|
292
|
350
|
83%
|
258
|
287
|
90%
|
|
Rhesus lymphocryptovirus
|
0
|
22
|
0%
|
1
|
16
|
6%
|
|
Rhesus monkey rhadinovirus
|
0
|
11
|
0%
|
0
|
7
|
0%
|
|
Saccharum officinarum
|
10
|
10
|
100%
|
16
|
16
|
100%
|
|
Saguinus labiatus
|
40
|
40
|
100%
|
42
|
42
|
100%
|
|
Schmidtea mediterranea
|
1
|
73
|
1%
|
4
|
63
|
6%
|
|
Selaginella moellendorffii
|
5
|
60
|
8%
|
14
|
58
|
24%
|
|
Simian virus 40
|
2
|
2
|
100%
|
1
|
1
|
100%
|
|
Sorghum bicolor
|
39
|
39
|
100%
|
72
|
72
|
100%
|
|
Sus scrofa
|
53
|
53
|
100%
|
55
|
55
|
100%
|
|
Symphalangus syndactylus
|
4
|
10
|
40%
|
5
|
11
|
46%
|
|
Tetraodon nigroviridis
|
108
|
109
|
99%
|
132
|
132
|
100%
|
|
Triticum aestivum
|
8
|
31
|
26%
|
9
|
32
|
28%
|
|
Vitis vinifera
|
41
|
79
|
52%
|
116
|
140
|
83%
|
|
Xenopus laevis
|
7
|
7
|
100%
|
7
|
7
|
100%
|
|
Xenopus tropicalis
|
130
|
166
|
78%
|
160
|
184
|
87%
|
|
Zea mays
|
43
|
43
|
100%
|
96
|
96
|
100%
|
|
Total Coverage
|
4193
|
6073
|
69%
|
4882
|
6396
|
76%
|
1. Perfect match to unique Sanger microRNA sequences
The values reported as “Sanger 11.0” 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 11.0" 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 the Affymetrix GeneChip platform.
The comprehensive content of 13,349 unique known and predicted miRNA mature sequences
were selected from miRBase release 9.2 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).