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Platform GPL2896 Query DataSets for GPL2896
Status Public on Sep 29, 2005
Title GE Healthcare/Amersham Biosciences CodeLink™ Rat Whole Genome Bioarray
Technology type spotted oligonucleotide
Distribution commercial
Organism Rattus norvegicus
Manufacturer GE Healthcare
Manufacture protocol 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).
Catalog number 300031
Support glass
Coating other
 
Description 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.
 
Submission date Sep 26, 2005
Last update date Jun 06, 2014
Contact name Randall Lockner
E-mail(s) randall.lockner@ge.com
Phone 480-722-2311
Fax 480-722-2334
URL http://www.codelinkbioarrays.com
Organization name GE Healthcare Life Sciences
Department Bioinformatics
Street address 7700 S River Parkway
City Tempe
State/province AZ
ZIP/Postal code 85284
Country USA
 
Samples (313) GSM100182, GSM100183, GSM100184, GSM100185, GSM131992, GSM131993 
Series (19)
GSE4458 Effer/Affer Interaction in Vestibular Caliceal vs. Dimorphic and Bouton Primary Afferent Neurons
GSE5350 MicroArray Quality Control (MAQC) Project
GSE9684 Trophic Factor Gene Expression in Supporting Cells of the Crista Ampullaris:Implications for Hair Cell Regeneration

Data table header descriptions
ID
LOGICAL_ROW The logical row position of the spot.
LOGICAL_COL The logical column position of the spot.
PROBE_NAME The unique probe identifier. Each Probe Name is specific for a given oligonucleotide probe and is the primary identifier.
PROBE_TYPE A classifier indicating the functional role of the oligonucleotide probe.
PUB_PROBE_TARGETS 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.
SPOT_ID An identifier for oligonucleotide probes that do not have a corresponding public reference.
GB_LIST 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)
GI_LIST 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)

Data table
ID LOGICAL_ROW LOGICAL_COL PROBE_NAME PROBE_TYPE PUB_PROBE_TARGETS SPOT_ID GB_LIST GI_LIST
1001 1 1 GE200017 FIDUCIAL CONTROL -- FID CTRL: PCTRL17
1002 1 2 GE1275839 DISCOVERY SINGLE CB717085.1 29774233
1003 1 3 GE1103838 MASK MASK -- MASK
1004 1 4 GE1204628 DISCOVERY SINGLE CB613942.1 29573830
1005 1 5 GE1289537 DISCOVERY SINGLE BF398129.1 11383115
1006 1 6 GE1250992 DISCOVERY SINGLE BG377995.1 13302467
1007 1 7 GE200017 FIDUCIAL CONTROL -- FID CTRL: PCTRL17
1008 1 8 GE200018 FIDUCIAL CONTROL -- FID CTRL: PCTRL18
1009 1 9 GE1101647 DISCOVERY SINGLE CB585517.1 29529558
1010 1 10 GE1125512 DISCOVERY SINGLE CB718094.1 29775242
1011 1 11 GE1109682 DISCOVERY SINGLE CB726355.1 29793287
1012 1 12 GE1246012 DISCOVERY SINGLE BF395764.1 11380735
1013 1 13 GE1265640 DISCOVERY SINGLE BM385989.1 18186042
1014 1 14 GE200018 FIDUCIAL CONTROL -- FID CTRL: PCTRL18
1015 1 15 GE200019 FIDUCIAL CONTROL -- FID CTRL: PCTRL19
1016 1 16 GE1301596 DISCOVERY SINGLE CB608348.1 29547961
1017 1 17 GE1251788 DISCOVERY SINGLE BF394429.1 11379295
1018 1 18 GE1162915 DISCOVERY SINGLE BM391627.1 18191680
1019 1 19 GE1300064 DISCOVERY SINGLE BF567346.1 11677076
1020 1 20 GE1164189 DISCOVERY SINGLE NM_207594.1 46485428

Total number of rows: 36736

Table truncated, full table size 2179 Kbytes.






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