Rat Bioarrays

CodeLink Rat Whole Genome Bioarray
The Rat Whole Genome Bioarray targets ~34 000 transcripts and ESTs, including over 29,000 well-annotated rat genes.

CodeLink Rat Focused Bioarrays

CodeLink Rat Focused Bioarrays provide the researcher with subsets of the whole genome array to enable pathway and process specific research.

Applied Microarrays will partner with you to create the required subset of interest.

In addition, we offer catalog Inflammation and ADME subsets which have been compiled in collaboration with expert researchers from that field.

Fig. CodeLink Rat Whole Genome Bioarrays exhibit excellent array-to-array signal intensity reproducibility. The plotted normalized probe signals from two independent CodeLink Rat 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 dark blue data points represent the concordantly "good" probes (G); the bright pink data points represent the non-concordantly "good" probes (G and L); and the light pink data points represent the concordantly "absent" probes (L). The two-fold lines are shown in gray.

Fig. CodeLink Rat Whole Genome Bioarrays ensure high differential expression ratio reproducibility for robust expression profiling. The normalized probe signals from four independent CodeLink Rat Whole Genome Bioarrays-two run with 10 µg of brain and two run with 10 ug of liver cRNA target-were used to calculate two separate data populations of brain:liver expression ratios. The log2 of those ratios are shown here. The dark blue data points represent the ratios generated from only concordantly "good" probes (G) on all of the bioarrays (n=21 347 ratios). The red line illustrates a slope of 1.

Specifications

The CodeLink Rat Whole Genome Bioarray is designed to interrogate approximately 34 000 transcripts representing most of the known and predictive genes of the rat genome, as it is described today in the public domain. Each transcript is represented by a 30-mer probe which is designed to conserved exons across the transcripts of targeted genes. The probe sequences, representing well annotated, full length and partial rat gene sequences, were designed based on sequences selected from the NCBI UniGene build #129, RefSeq database (April 1, 2004 release) and dbEST database (March 20, 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 95% were functionally validated against 10 rat tissues to ensure best representation of the gene and biologically relevant results.

Probe distribution

product specifications

 

expression bioarrays

 

CodeLink Rat Whole Genome Bioarray

 

CodeLink™ Rat Whole Genome Bioarray has 33,849 discovery probes representing up to 32,590 unique transcripts. The transcript sequences were selected from the NCBI UniGene build #129, the RefSeq database (April 1, 2004 release), and the dbEST database (March 20, 2004 release). In addition to the discovery probe sequences, each bioarray contains positive and negative bacterial control probes for monitoring array performance. All oligonucleotide probes are 30 bases long.

Probe sets	Probes/gene	Redundancy	Dispense count
Number of rat probes	33,849 unique sequences	1	33,849 probes
Positive bacterial control probes	5 probes/gene × 6 bacterial targets	8	240 probes
Negative bacterial control probes	32 negative control probes	8	256 probes
TOTAL			34,345 probes

Performance specifications

 

The following data are based on results from the final product verification studies conducted using a series of bioarrays and targets generated from rat tissue.

Performance parameter	Performance requirement	Verified assay performance
Specificity	Discrimination > 2 base mismatches	Discrimination > 2 base mismatches
Sensitivity	1:1,024,000 mass ratio (bacterial spike)*	1:2,048,000 mass ratio (bacterial spike) with cRNA spiking at the cRNA level*, **
Dynamic range	Linear signal response over two orders of magnitude	Linear signal response over three orders of magnitude; 0.05 pM – 50 pM
Signal reproducibility (total CV)	< 20% total median CV	8.8% total median CV across production batches 7.9% median CV for all spots excluding spots below noise
Minimum detectable fold change	95% within two‐fold change for the same tissue	98.8% within two‐fold change for the same tissue for all good spots across different production batches
Input sample	0.1 µg – 2 µg total RNA	0.1– 2.0 µg total RNA***

* mass ratio spiking of cRNA control spike into cRNA target

** the lowest level tested in verification experiments with cRNA spiking

*** generates sufficient amplified material for 1‐8 replicates depending on tissue and starting amount

Storage and handling conditions

 

Upon receipt, store CodeLink™ Rat Whole Genome Bioarrays with desiccant at room temperature.

Safety precautions

 

 

Standard laboratory safety procedures should be followed when using this product. Safety glasses, a lab coat, and appropriate gloves should be worn at all times when in the laboratory.