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Platform GPL2112 Query DataSets for GPL2112
Status Public on May 24, 2005
Title [Bovine] Affymetrix Bovine Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Bos taurus
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/projects/geo/info/geo_affy.html

The GeneChip Bovine Genome Array can be used to study gene expression of over 23,000 bovine transcripts. The array is an ideal tool for researchers studying gene expression profiles in cattle. With the broadest representation of publicly available expressed sequence information, bovine researchers will be able to use this array to monitor genetic mechanisms regulating a variety of preferred traits, such as:

- Disease resistance
- Meat and dairy production
- Stress tolerance

The Bovine Genome Array was designed in close collaboration with the Bovine Research Community as part of the Affymetrix GeneChip Consortia Program.

Annotations derived from Affymetrix CSV file dated 4/01/2005

 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=bovine
http://www.affymetrix.com/analysis/index.affx
Submission date May 23, 2005
Last update date Dec 17, 2012
Organization Affymetrix, Inc.
E-mail(s) geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (2294) GSM52151, GSM52152, GSM77670, GSM77671, GSM77672, GSM77673 
Series (133)
GSE2704 Comparison of bovine gd and ab T cell clones
GSE3439 Profiling of mucosal derived bovine ab and gd T cells during Salmonella enterica serovar typhimurium enterocolitis
GSE5195 Analysis of gene expression during the onset of muscle hypertrophy in callipyge lambs: time course
Relations
Alternative to GPL10186 (Alternative CDF)
Alternative to GPL10941 (Alternative CDF)
Alternative to GPL13706 (Alternative CDF)

Data table header descriptions
ID Affymetrix Probe Set ID
Species Scientific Name The genus and species of the organism represented by the probe set.
GB_ACC GenBank Accession Number
SPOT_ID spot identifier
GI GenBank GI Number
UniGene ID UniGene accession number.
Gene Title Title of Gene represented by the probe set.
Gene Symbol A gene symbol, when one is available (from UniGene).
Annotation Date The date that the annotations for this probe array were last updated. It will generally be earlier than the date when the annotations were posted on the Affymetrix web site.
Sequence Type Indicates whether the sequence is an Exemplar, Consensus or Control sequence. An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database.
Sequence Source The database from which the sequence used to design this probe set was taken.
Transcript ID(Array Design)
Target Description GenBank description associated with the representative public identifier. Blank for some probe sets.
Representative Public ID The accession number of a representative sequence. Note that for consensus-based probe sets, the representative sequence is only one of several sequences (sequence sub-clusters) used to build the consensus sequence and it is not directly used to derive the probe sequences. The representative sequence is chosen during array design as a sequence that is best associated with the transcribed region being interrogated by the probe set. Refer to the "Sequence Source" field to determine the database used.
Archival UniGene Cluster UniGene cluster ID, curated at the time of array design, of the group of sequences used to build the consensus sequence.
Chromosomal Location Chromosomal location. We add the prefix "Chr:" to avoid problems with some spreadsheet applications interpreting some locations as Dates.
Unigene Cluster Type
ENTREZ_GENE_ID Entrez Gene Database UID
RefSeq Protein ID ID of the protein sequence in the NCBI RefSeq database.
RefSeq Transcript ID References to multiple sequences in RefSeq. The field contains the ID and Description for each entry, and there can be multiple entries per ProbeSet.
Annotation Description Annotation description

Data table
ID Species Scientific Name GB_ACC SPOT_ID GI UniGene ID Gene Title Gene Symbol Annotation Date Sequence Type Sequence Source Transcript ID(Array Design) Target Description Representative Public ID Archival UniGene Cluster Chromosomal Location Unigene Cluster Type ENTREZ_GENE_ID RefSeq Protein ID RefSeq Transcript ID Annotation Description
AFFX-BioB-3_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioB E. coli /GEN=bioB /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 2755-3052 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioB-3 This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-BioB-5_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioB E. coli /GEN=bioB /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 2032-2305 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioB-5 This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-BioB-M_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioB E. coli /GEN=bioB /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 2482-2739 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioB-M This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-BioC-3_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioC E. coli /GEN=bioC /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 4626-4878 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioC-3 This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-BioC-5_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioC E. coli /GEN=bioC /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 4218-4566 of gb:J04423.1 /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioC-5 This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-BioDn-3_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioD E. coli /GEN=bioD /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 5286-5570 of gb:J04423.1, not 100% identical /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioDn-3 This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-BioDn-5_at Bos taurus J04423.1 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AFFX-Ec-bioD E. coli /GEN=bioD /DB_XREF=gb:J04423.1 /NOTE=SIF corresponding to nucleotides 4980-5256 of gb:J04423.1, not 100% identical /DEF=E.coli 7,8-diamino-pelargonic acid (bioA), biotin synthetase (bioB), 7-keto-8-amino-pelargonic acid synthetase (bioF), bioC protein, and dethiobiotin synthetase (bioD), complete cds. AFFX-BioDn-5 This probe set was annotated using the Matching Probes based pipeline to a Blattner identifier using 1 transcripts. // false // Matching Probes // A
AFFX-Bt-A00196-1_s_at Bos taurus A00196 31-Mar-05 Consensus sequence Affymetrix Proprietary Database A00196-1 CONTROL A00196 /FEA=CDS /DB_XREF=CAA00038.1 GI:14446 REMTREMBL:CAA00038 /PROD=beta glucuronidase /GEN=uidA AFFX-Bt-A00196-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AB076373-1_at Bos taurus AB076373 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AB076373-1 CONTROL AB076373 /FEA=CDS_1 /DB_XREF=BAC00955.1 GI:21623749 /PROD=thiazole synthase /GEN=ptrA AFFX-Bt-AB076373-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-actin-3_at Bos taurus NM_174225.1 8435 actin, alpha 1, skeletal muscle ACTA1 31-Mar-05 Consensus sequence GenBank Bt.8435.1 CONTROL gb:NM_174225.1 /DB_XREF=gi:27819613 /GEN=ACTA1 /TID=Bt.8435.1 /CNT=266 /FEA=FLmRNA /TIER=FL+Stack /STK=23 /LL=281592 /UG=Bt.8435 /DEF=Bos taurus actin, alpha 1, skeletal muscle (ACTA1), mRNA. /PROD=actin, alpha 1, skeletal muscle /FL=gb:NM_174225.1 NM_174225.1 Bt.8435 281592 NP_776650.1 NM_174225 This probe set was annotated using the Matching Probes based pipeline to a Locus Link identifier using 1 transcripts. // false // Matching Probes // A
AFFX-Bt-actin-5_at Bos taurus NM_174225.1 8435 actin, alpha 1, skeletal muscle ACTA1 31-Mar-05 Consensus sequence GenBank Bt.8435.1 CONTROL gb:NM_174225.1 /DB_XREF=gi:27819613 /GEN=ACTA1 /TID=Bt.8435.1 /CNT=266 /FEA=FLmRNA /TIER=FL+Stack /STK=23 /LL=281592 /UG=Bt.8435 /DEF=Bos taurus actin, alpha 1, skeletal muscle (ACTA1), mRNA. /PROD=actin, alpha 1, skeletal muscle /FL=gb:NM_174225.1 NM_174225.1 Bt.8435 281592 NP_776650.1 NM_174225 This probe set was annotated using the Matching Probes based pipeline to a Locus Link identifier using 1 transcripts. // false // Matching Probes // A
AFFX-Bt-actin-M_at Bos taurus NM_174225.1 8435 actin, alpha 1, skeletal muscle ACTA1 31-Mar-05 Consensus sequence GenBank Bt.8435.1 CONTROL gb:NM_174225.1 /DB_XREF=gi:27819613 /GEN=ACTA1 /TID=Bt.8435.1 /CNT=266 /FEA=FLmRNA /TIER=FL+Stack /STK=23 /LL=281592 /UG=Bt.8435 /DEF=Bos taurus actin, alpha 1, skeletal muscle (ACTA1), mRNA. /PROD=actin, alpha 1, skeletal muscle /FL=gb:NM_174225.1 NM_174225.1 Bt.8435 281592 NP_776650.1 NM_174225 This probe set was annotated using the Matching Probes based pipeline to a Locus Link identifier using 1 transcripts. // false // Matching Probes // A
AFFX-Bt-AF292559-1_at Bos taurus AF292559 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF292559-1 CONTROL AF292559 /FEA=CDS_1 /DB_XREF=AAG34044.1 GI:11321077 /PROD=yellow fluorescent protein yfp /GEN=yfp AFFX-Bt-AF292559-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AF292559-2_s_at Bos taurus AF292559 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF292559-2 CONTROL AF292559 /FEA=CDS_2 /DB_XREF=AAG34045.1 GI:11321078 /PROD=mob /GEN=mob AFFX-Bt-AF292559-2 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AF292559-3_s_at Bos taurus AF292559 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF292559-3 CONTROL AF292559 /FEA=CDS_3 /DB_XREF=AAG34046.1 GI:11321079 /PROD=repB /GEN=repB AFFX-Bt-AF292559-3 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AF292559-4_s_at Bos taurus AF292559 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF292559-4 CONTROL AF292559 /FEA=CDS_4 /DB_XREF=AAG34047.1 GI:11321080 /PROD=kanamycin resistance protein /GEN=aphA AFFX-Bt-AF292559-4 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AF292560-1_s_at Bos taurus AF292560 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF292560-1 CONTROL AF292560 /FEA=CDS_1 /DB_XREF=AAG34048.1 GI:11321082 /PROD=cyan fluorescent protein cfp /GEN=cfp AFFX-Bt-AF292560-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AF298789-1_at Bos taurus AF298789 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF298789-1 CONTROL AF298789 /FEA=CDS_1 /DB_XREF=AAG34533.1 GI:11344896 /PROD=phosphoribosylanthranilate isomerase /GEN=TRP1 AFFX-Bt-AF298789-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AF323980-1_at Bos taurus AF323980 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AF323980-1 CONTROL AF323980 /FEA=CDS /DB_XREF=AAK26531.1 GI:13446782 /PROD=minor outer capsid protein VP4 /NOTE=viral protein 4 AFFX-Bt-AF323980-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //
AFFX-Bt-AJ002682-1_s_at Bos taurus AJ002682 31-Mar-05 Consensus sequence Affymetrix Proprietary Database AJ002682-1 CONTROL AJ002682 /FEA=CDS_1 /DB_XREF=CAA05684.1 GI:2623979 REMTREMBL:CAA05684 /GEN=kanamycin resistance gene AFFX-Bt-AJ002682-1 No current annotation is available for this probe set at this time. Only library file information is available. // // //

Total number of rows: 24128

Table truncated, full table size 12811 Kbytes.






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