Mouse Bioarrays for Gene Expression

CodeLink™ Mouse Whole Genome Bioarray (~36 000 mouse gene targets)
CodeLink UniSet™ Mouse 20K I Bioarray (~20 000 mouse gene targets)
CodeLink UniSet Mouse I Bioarray (~10 000 mouse gene targets)


CodeLink™ Mouse Whole Genome Bioarray offers comprehensive genome-wide gene expression analysis on a single bioarray.

Accurate and reproducible biological results. For best results from every bioarray experiment, ~36 000 quality probes were designed and experimentally tested for performance. In addition, advanced non-contact deposition robots and Six Sigma based manufacturing processes ensure that every CodeLink bioarray complies to design and quality specifications.

High assay sensitivity and specificity. An improved and proprietary 3-D aqueous gel matrix ensures enhanced interaction between probe and target simulating liquid phase hybridization kinetics. With this new matrix, sensitivity of detection is as low as 1:2 000 000 mass ratio determined by spiking experiments at the cRNA level for enhanced detection of low abundance transcripts.

	Typical performance	Benefit
Sensitivity	Mass ratio <1:1 000 000 with bacterial spiking into cRNA or total RNA level	Detection of more low abundance transcripts (<0.3 copies per cell)
Dynamic range	Linear signal response across three orders of magnitude (0.05 pM – 50 pM)	More usable/accurate data across a broad range of gene expression levels
Specificity	Discrimination of >2 base mismatches	Better discrimination of highly homologous genes
Signal reproducibility	Typically <15% total median CV among production batches, all probes included; ~8% median CV among production batches, only probes above noise included	Reproducible differential expression results in every experiment
Minimum detectable fold change	>98% within two-fold change for replicates	Reduced noise for better detection of small changes in gene expression and more usable data per bioarray

Fig. CodeLink Whole Genome Bioarrays show sensitivity of detection down to ~1:2 000 000 mass ratio determined by spiking experiments at the cRNA. Total dynamic range shown is 0.05-50 pM spike concentration range. ..

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Fig. CodeLink Mouse Whole Genome Bioarrays exhibit excellent array to array signal intensity reproducibility. A. The plotted normalized probe signals from two independent CodeLink Mouse Whole Genome Bioarrays—each run with 10 µg of the same labeled brain cRNA target—are shown here. Between these two bioarrays, 99.6% of all probes with “good” signals were within two-fold of each other. The blue data points represent the concordantly “good” probes; the red data points represent the concordantly “absent” probes. The two-fold lines are shown in gray. ..

Fig. CodeLink Mouse Whole Genome Bioarrays exhibit excellent reproducibility within and across bioarray production batches as represented by median % CV. These data were generated using one brain cRNA sample on three replicate arrays from one production batch (within batch, blue), and one array from each of three production batches (across batch, red). ..

Specifications

Mice exhibit high similarity to many human biological pathways, making it a key model system for human physiological and toxicological studies in drug discovery applications. The probe sequences, representing well annotated, full length and partial mouse gene sequences, were designed based on sequences selected from the NCBI UniGene build #139, RefSeq database (April 1, 2004 release) and dbEST database (July 31, 2004 release).Well-annotated mRNA or coding sequences were chosen to ensure usefulness for a large range of applications in basic research, biotechnology, and drug development. Each sequence was carefully screened to ensure high-quality, specific probe design, and to reduce redundancy of gene targets. All of the probes designed to these sequences were functionally tested, and over 97% were functionally validated against 14 mouse tissues to ensure best representation of the gene and biologically relevant results.

Number of arrays in set	1
Number of probes	35 587 (Total) 34 967 (Unique sequences)
Number of transcripts	36 142
Number of probes targeting transcripts other than controls	34 967
Positive controls	300
Negative controls	320
Housekeeping genes	~50
Number of probes per gene	One specific and functionally validated probe
Oligonucleotide probe length	30-mer probe
Probe proximity to 3' end	90% within 939 bases; average distance of 412 bases
Total RNA input	0.2–2 µg total RNA
cRNA input	10 µg
Type of assay	One color
Storage and handling temperature	Room temperature

Back-compatible data

For flexibility and data preservation, CodeLink Mouse Whole Genome Bioarrays are compatible with lower density CodeLink mouse bioarrays. This means that existing data from CodeLink UniSet Mouse 20K Bioarrays can be continuously used in
future studies along with newly generated data from CodeLink Mouse Whole Genome Bioarrays.

Fig. CodeLink Mouse Whole Genome Bioarrays generate data that is back-compatible to corresponding data from CodeLink UniSet Mouse 20K Bioarrays. The differential expression ratios of brain to ovary show high concordance between the two CodeLink Bioarray platforms. The normalized probe signals from two bioarrays of each CodeLink product and of each cRNA target (brain and ovary) were averaged separately. The brain:ovary ratios of these mean normalized signals were then calculated for each product: CodeLink Mouse Whole Genome Bioarray and CodeLink UniSet Mouse 20K Bioarray. The log2 of those ratios from the two products’ overlapping subset of probes are shown here. The dark blue data points represent the ratios generated from only concordantly “good” probes (G) on all of the bioarrays (n = 9559 ratios). The red line illustrates a slope of 1. ..

CodeLink UniSet Mouse Bioarrays

CodeLink UniSet Mouse Bioarrays deliver superior results through:

• quality probe design and selection that includes functional validation for accurate and reproducible biological results
• manufacturing process control checkpoints to ensure probe and deposition quality for reproducible experimental results
• unique three-dimensional aqueous gel matrix for higher assay sensitivity and specificity
• optimized reagents, protocols, processing tools, and software for ease of use and reliable performance

• ~10 000 mouse genes — 1 specific, prescreened probe per gene, functionally validated
• one set of housekeeping genes that may be used for baseline normalization
• 18 bacterial positive control probes from 6 genes with 6 corresponding spikes included in the cDNA Synthesis Kit to monitor