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.
For flexibility and data preservation, CodeLink Rat Whole Genome Bioarrays are compatible with lower density CodeLink rat bioarrays. This means that existing data from CodeLink UniSet™ Rat 10K Bioarrays can be continuously used in future studies along with newly generated data from CodeLink Rat Whole Genome Bioarrays.
CodeLink users can submit data to GEO by exporting tab-delimited text files from the CodeLink software. The "Feature_id" header will need to be renamed to "ID_REF", and the "Normalized_intensity" header to "VALUE" before uploading the exported tables.
In addition, users are encouraged to include additional raw data columns in their data uploads. These additional columns do not need to be renamed.
Transcriptomic response in the heart and kidney to different types of antihypertensive drug administration
Data table header descriptions
The logical row position of the spot.
The logical column position of the spot.
The unique probe identifier. Each Probe Name is specific for a given oligonucleotide probe and is the primary identifier.
A classifier indicating the functional role of the oligonucleotide probe.
A classifier describing the oligonucleotide probe to target relationship. SINGLE - the oligo uniquely targets a single transcript in the public domain. MULTIPLE - the oligo targets more than one transcript in the public domain. DUPLICATE - more than one oligo exists on the bioarray that target the same transcript.
An identifier for oligonucleotide probes that do not have a corresponding public reference.
NCBI GenBank accession numbers. Multiple accessions are listed for probes having more than one target transcript (the first accession in the list is the primary accession assigned to the target sequence)
NCBI GenBank GI numbers. Multiple GI numbers are listed for probes having more than one target transcript (the first GI number in the list is the primary GI assigned to the target sequence)