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Platform GPL2895 Query DataSets for GPL2895
Status Public on Sep 29, 2005
Title GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray
Technology type spotted oligonucleotide
Distribution commercial
Organism Homo sapiens
Manufacturer GE Healthcare
Manufacture protocol http://www4.amershambiosciences.com/aptrix/upp01077.nsf/Content/codelink_user_protocols
Catalog number 300026
Support glass
Coating other
 
Description CodeLink Human Whole Genome Bioarray targets most of the known and predictive genes of the human genome as it is described today in the public domain. It is comprised of approximately 55 000 30-mer probes designed to conserved exons across the transcripts of targeted genes. These 55 000 probes represent well annotated, full length, and partial human gene sequences from major public databases. CodeLink Human Whole Genome Bioarray probe sequences were selected from the NCBI UniGene build #165, RefSeq database (January 5, 2004 release) and dbEST database (January 8, 2004 release). Some sequences for design were derived from Incyte LifeSeqâ„¢ Gold and Foundation databases.

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 80% were functionally validated against 25 human tissues to ensure best representation of the gene and biologically relevant results.

As a result of their high-quality probe content and design, CodeLink Human Whole Genome Bioarrays are useful for performing differential expression studies of many important biological processes in a single experiment. For instance, CodeLink Human Whole Genome Bioarray can be used to study unique gene expression profiles at different stages of oncogenesis. These studies help to characterize and understand tumor types and tumor progression for use in drug target identification and personalized medicine. In addition, this bioarray enables the investigation of cell and tissue reactions to their environment from stimulus reception to signal transduction processing and response. This bioarray comprehensively covers cell differentiation, development, apoptosis, and metabolism for drugs and other cellular biomolecules.

Expression profiling of the genes involved in these types of biological processes can be directly applied to target identification, pathway characterization, and drug effect prediction in basic research and drug development.

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_human_bioarrays#Whole
Submission date Sep 26, 2005
Last update date Oct 28, 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 (1589) GSM82284, GSM82285, GSM82286, GSM82287, GSM82288, GSM82289 
Series (69)
GSE3578 Activated Cell Death Pathway
GSE4106 Gene expression induced by Nanosecond pulsed electric fields
GSE4609 Transcriptome analysis of Stem Cells from Human Umbilical Cord Blood
Relations
Alternative to GPL11010
Alternative to GPL8060
Alternative to GPL18134 ([DISCOVERY PROBE_TYPE])

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 GE766244 DISCOVERY SINGLE XM_293099.2 30157495
1003 1 3 GE766859 DISCOVERY SINGLE BF588963.1 11681287
1004 1 4 GE519376 DISCOVERY SINGLE -- NP DISC: INCYTE UNIQUE
1005 1 5 GE519777 DISCOVERY SINGLE BE550764.1 9792456
1006 1 6 GE895719 DISCOVERY SINGLE AK095554.1 21754831
1007 1 7 GE896168 DISCOVERY SINGLE BG260785.1 12770601
1008 1 8 GE200018 FIDUCIAL CONTROL -- FID CTRL: PCTRL18
1009 1 9 GE768684 DISCOVERY SINGLE BF763000.1 12110900
1010 1 10 GE769330 DISCOVERY SINGLE AA632993.1 2556407
1011 1 11 GE521062 DISCOVERY SINGLE -- NP DISC: INCYTE UNIQUE
1012 1 12 GE521431 DISCOVERY SINGLE AK122611.1 34527787
1013 1 13 GE897528 DISCOVERY SINGLE AW449311.1 6990087
1014 1 14 GE897998 DISCOVERY SINGLE BF029356.1 10737068
1015 1 15 GE200019 FIDUCIAL CONTROL -- FID CTRL: PCTRL19
1016 1 16 GE766257 DISCOVERY SINGLE AA579187.1 2357371
1017 1 17 GE766861 DISCOVERY SINGLE AA572949.1 2347477
1018 1 18 GE519380 DISCOVERY SINGLE BX101031.1 27844680
1019 1 19 GE519781 DISCOVERY SINGLE BX116239.1 27839853
1020 1 20 GE895725 DISCOVERY SINGLE AI580480.1 4564856

Total number of rows: 56448

Table truncated, full table size 3457 Kbytes.






Download family Format
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Supplementary data files not provided

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