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Platform GPL2897 Query DataSets for GPL2897
Status Public on Sep 29, 2005
Title GE Healthcare/Amersham Biosciences CodeLinkā„¢ Mouse Whole Genome Bioarray
Technology type spotted oligonucleotide
Distribution commercial
Organism Mus musculus
Manufacturer GE Healthcare
Manufacture protocol http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_user_protocols
Catalog number 300033
Support glass
Coating other
 
Description 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.
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.

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.

 
Web link http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_uniset_mouse1_bioarray
Submission date Sep 26, 2005
Last update date Mar 25, 2013
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 (676) GSM83090, GSM83100, GSM83101, GSM83102, GSM83103, GSM83104 
Series (37)
GSE3603 Microarray analysis of in vivo inhibition of mir-122 with an antisense oligonucleotide.
GSE4221 Wildtype Mouse Hypothalamus Cerebellum Fed Fast
GSE5331 Radiation-induced genes expressed in two murine tumors.
Relations
Affiliated with GPL16865

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 GE1488331 DISCOVERY SINGLE NM_207255.1 46402262
1003 1 3 GE1461340 DISCOVERY SINGLE -- NP DISC: CODELINK UNIQUE
1004 1 4 GE1415502 DISCOVERY SINGLE AK080548.1 26099320
1005 1 5 GE1560236 DISCOVERY SINGLE BM115361.1 17078379
1006 1 6 GE1557210 DISCOVERY SINGLE AK015221.1 12853475
1007 1 7 GE200017 FIDUCIAL CONTROL -- FID CTRL: PCTRL17
1008 1 8 GE200018 FIDUCIAL CONTROL -- FID CTRL: PCTRL18
1009 1 9 GE1406184 MASK SINGLE -- MASK
1010 1 10 GE1409715 DISCOVERY SINGLE BX636603.1 33616478
1011 1 11 GE1417824 MASK SINGLE -- MASK
1012 1 12 GE1572262 DISCOVERY SINGLE AK047664.1 26092339
1013 1 13 GE1537512 DISCOVERY SINGLE CA879667.1 27331216
1014 1 14 GE200018 FIDUCIAL CONTROL -- FID CTRL: PCTRL18
1015 1 15 GE200019 FIDUCIAL CONTROL -- FID CTRL: PCTRL19
1016 1 16 GE1446262 MASK SINGLE -- MASK
1017 1 17 GE1388074 DISCOVERY SINGLE BF160755.1 11040862
1018 1 18 GE1425706 DISCOVERY SINGLE BC041149.1 27370741
1019 1 19 GE1514303 DISCOVERY SINGLE AA822155.1 2892023
1020 1 20 GE1575536 DISCOVERY SINGLE BC048760.1 28908263

Total number of rows: 45920

Table truncated, full table size 2656 Kbytes.






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Supplementary data files not provided

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