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.
| Number of arrays in set | 1 |
| Number of probes | 33 849 |
| Number of transcripts | 32 590 |
| Number of discovery genes | 29 842 (Based on unique UniGene IDs) |
| Positive controls | 240 |
| Negative controls | 256 |
| 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 550 bases; average distance of 289 bases |
| RNA sample input | 0.2–2 µg total RNA |
| Type of assay | One color |
| Storage and handling temperature | Room temperature |
| temperature |
Probe distribution
| Unique NCBI accession numbers | 32 590 |
| Unique NCBI accession numbers | 32 590 |
| Unique UniGene IDs | 29 842 |
| Unique RefSeq IDs | 4212 |
| Unique locus link IDs | 12 449 |
| Ensembl genes | 4000 |