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Over 30,000 Probes Give You
a Wealth of Information!
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Each probe is spotted onto the array in a highly consistent manner using an innovative non-contact spotting technology adapted and perfected by Phalanx Biotech for microarray manufacturing.
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Product Description and Overview
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The Mouse OneArray Whole Genome DNA microarray is made of sense-strand polynucleotide probes spotted onto a proprietary chemical layer coated on top of a 1" x 3" (25mm x 75mm) standard-format microarray glass slide. |
The Mouse OneArray probe set is an abridged version of the Mouse Exonic Evidence Based Oligonucleotide (MEEBO) probe set developed at Stanford and UCSF. Our abridged version has eliminated a large number of splice variants and outdated ESTs to optimize the identification of relevant genes. This provides the most efficient probe set and the best value in mouse genome microarrays. |
Mouse OneArray Genome Content
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- Each microarray contains 31,802 oligonucleotides: 29,922 mouse genome probes, and 1880 experimental control probes.
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- Mouse OneArray content is based on an abridged version of the Mouse Exonic Evidence Based Oligonucleotide (MEEBO)*.
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- For more information about MEEBO, please access the following Web site:
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http://arrays.ucsf.edu/archive/meebo.html
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| *Special thanks to Dr. John Coller for his helpful discussion in the selection of probe sets for reduction. |
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| Mouse OneArray™ Probe Content |
| Probe Type |
Number of Probes |
| MEEBO (abridged version) |
29,922 (total)* |
Group Code: MC
Mouse constitutive exonic: Rockefeller MouSDB3
Constitutive exons and locuslink2ucsf constitutive exons |
24,858 |
Group Code: MR
Mouse mRNAs: mRNA derived 70-mer probes, which may span >1 exon |
5064 |
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*Mouse OneArray is guaranteed to have >98% of the total probe content printed. |
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Table 1: Mouse Genome Content |
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Mouse OneArray Control Features
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Grid Alignment Mark (GAM) |
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- Probe ID Number: PH_0000001
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GAM control probe is a Cy3 labeled 60-mer oligonucleotide probe designed from an alien sequence that does not cross-hybridize with mouse targets. More than 90 GAM features are evenly distributed across the arrayed area, and these features can be excited by a 532 nm laser without hybridization. GAM probes can serve as orientation or grid-alignment landmarks.
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Orientation Grid Alignment Mark (OGAM) |
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- Probe ID Number: PH_c_0000089
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OGAM is a Cy3/Cy5 labeled 60-mer oligonucleotide probe designed from an alien sequence that does not cross-hybridize with mouse targets. It is located on top of the upper left cornerof the print region and serves as an orientation landmark for template registration asdifferent scanners may have different image orientation output formats. Figure 2, below,illustrates this.
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Corner Grid Alignment Marks (CGAMs) |
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- Probe ID Number: PH_c_0000072
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CGAMs are mixtures of Cy3/Cy5 labeled 60-mer oligo designed from an alien sequence that does not cross-hybridize with mouse targets. CGAMs are located at the four corners of the image and serve as the orientation landmarks for auto or manual grid alignment under Cy3 (532 nm) or Cy5 (635 nm) scanning channel. Figure 2, below, illustrates this. |
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Figure 2: Mouse OneArray OGAM and CGAM Positions |
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Intrinsic Hybridization Controls (IHCs) |
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- Probe ID Number: PH_c_0000100
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IHCs contain mixtures of probes from 10 robustly expressed
house-keeping genes that serve as built-in positive controls (see
Table 3, below). The probe mixture is dispensed at a fixed concentration, and more than 95 IHC features are evenly distributed across the arrayed area. The hybridization signal intensity of IHCs gives the indication of overall quality of sample processing and hybridization efficiency. |
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Table 3: Mouse OneArray IHC Control Probe Information |
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Intrinsic Hybridization Ladder (IHL) |
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- Probe ID Numbers:
PH_c_0000101
to PH_c_0000116
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The IHL probes are dispensed in serial dilutions of IHC controls. The data extracted from IHL after target hybridization can be used to construct a hybridization intensity response curve depending on different dilutions of the probe mixture, which will be able to serve as an indicator to monitor the overall consistency of sample processing and hybridization stringency. Table 4, below, provides the ID number of the IHL controls and detailed information about their content. |
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Table 4: Mouse OneArray IHL Control Probe Data |
Negative Control/Extrinsic Target Quality Control (ETQC) |
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- Probe ID Numbers:
PH_c_0000066 to PH_c_0000071
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ETQC probes are alien probe sequences that do not cross-hybridize with mouse genomic probes on Mouse OneArray. The targets to these probes can be prepared separately as RNA containing a poly-A tail and spiked into the experimental RNA sample to monitor target preparation
quality and determine the sensitivity of the hybridization reaction. |
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- Probe ID Number: mCA 000xxx
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Probes recognizing the antisense strand of selected mouse and doping transcripts.
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- Probe ID Number: mCN 000xxx
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Probes are randomized 70-mer oligonucleotides selected not to recognize mouse genes. |
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- Probe ID Number: mCT 000xxx
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Series of probes designed to recognize sequences at varying distances from the 3' end, plus 11 mouse genes and selected spike-in transcripts. |
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