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Platform GPL3533 Query DataSets for GPL3533
Status Public on Mar 09, 2006
Title [Porcine] Affymetrix Porcine Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Sus scrofa
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The GeneChip Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome. The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.

The sequence information for this array was selected from public data sources including UniGene Build 28 (August 2004), GenBank® mRNAs up to August 24, 2004, and GenBank porcine mitochondrial and rRNA sequences. Probe sets consist of up to eleven probe pairs. The array format consists of eleven micron features synthesized on the 100 format.

Keywords = high density oligonucleotide array
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=porcine
http://www.affymetrix.com/analysis/index.affx
Submission date Mar 09, 2006
Last update date May 03, 2013
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 (3844) GSM100675, GSM100676, GSM100677, GSM100678, GSM100679, GSM100680 
Series (177)
GSE4474 Expression data from ovarian follicles in different developmental stages
GSE7313 Expression data from non-infected and Salmonella Typhimurium infected mesenteric lymph nodes
GSE7314 Expression data from non-infected and Salmonella Choleraesuis infected mesenteric lymph nodes

Data table header descriptions
ID Affymetrix Probe Set ID
GB_LIST GenBank Accession Number
Species Scientific Name The genus and species of the organism represented by the probe set.
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.
SPOT_ID 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.
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.
Gene Title Title of Gene represented by the probe set.
Gene Symbol A gene symbol, when one is available (from UniGene).
ENTREZ_GENE_ID Entrez Gene Database UID
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.
Gene Ontology Biological Process Gene Ontology Consortium Biological Process derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Cellular Component Gene Ontology Consortium Cellular Component derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Molecular Function Gene Ontology Consortium Molecular Function derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".

Data table
ID GB_LIST Species Scientific Name Annotation Date SPOT_ID Representative Public ID Gene Title Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
AFFX-BioB-3_at Sus scrofa Dec 19, 2005 Control AFFX-BioB-3 biotin synthesis, sulfur insertion? bioB 9102 // biotin biosynthesis // inferred from electronic annotation 3824 // catalytic activity // inferred from electronic annotation /// 4076 // biotin synthase activity // inferred from electronic annotation /// 5506 // iron ion binding // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation /// 46872 // metal ion binding // inferred from electronic annotation /// 51536 // iron-sulfur cluster binding // inferred from electronic annotation /// 51537 // 2 iron, 2 sulfur cluster binding // inferred from electronic annotation /// 51539 // 4 iron, 4 sulfur cluster binding // inferred from electronic annotation
AFFX-BioB-5_at Sus scrofa Dec 19, 2005 Control AFFX-BioB-5 Biotin synthase /// biotin synthesis, sulfur insertion? bioB 9102 // biotin biosynthesis // inferred from electronic annotation 3824 // catalytic activity // inferred from electronic annotation /// 4076 // biotin synthase activity // inferred from electronic annotation /// 5506 // iron ion binding // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation /// 46872 // metal ion binding // inferred from electronic annotation /// 51536 // iron-sulfur cluster binding // inferred from electronic annotation /// 51537 // 2 iron, 2 sulfur cluster binding // inferred from electronic annotation /// 51539 // 4 iron, 4 sulfur cluster binding // inferred from electronic annotation
AFFX-BioB-M_at Sus scrofa Dec 19, 2005 Control AFFX-BioB-M Biotin synthase /// biotin synthesis, sulfur insertion? bioB 9102 // biotin biosynthesis // inferred from electronic annotation 3824 // catalytic activity // inferred from electronic annotation /// 4076 // biotin synthase activity // inferred from electronic annotation /// 5506 // iron ion binding // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation /// 46872 // metal ion binding // inferred from electronic annotation /// 51536 // iron-sulfur cluster binding // inferred from electronic annotation /// 51537 // 2 iron, 2 sulfur cluster binding // inferred from electronic annotation /// 51539 // 4 iron, 4 sulfur cluster binding // inferred from electronic annotation
AFFX-BioC-3_at Sus scrofa Dec 19, 2005 Control AFFX-BioC-3 biotin biosynthesis; reaction prior to pimeloyl CoA bioC 9102 // biotin biosynthesis // inferred from electronic annotation 8168 // methyltransferase activity // inferred from electronic annotation /// 8757 // S-adenosylmethionine-dependent methyltransferase activity // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation
AFFX-BioC-5_at Sus scrofa Dec 19, 2005 Control AFFX-BioC-5 Biotin synthesis protein bioC /// biotin biosynthesis; reaction prior to pimeloyl CoA bioC 9102 // biotin biosynthesis // inferred from electronic annotation 8168 // methyltransferase activity // inferred from electronic annotation /// 8757 // S-adenosylmethionine-dependent methyltransferase activity // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation
AFFX-BioDn-3_at Sus scrofa Dec 19, 2005 Control AFFX-BioDn-3 dethiobiotin synthetase bioD 9102 // biotin biosynthesis // inferred from electronic annotation /// 9236 // cobalamin biosynthesis // inferred from electronic annotation 166 // nucleotide binding // inferred from electronic annotation /// 287 // magnesium ion binding // inferred from electronic annotation /// 4141 // dethiobiotin synthase activity // inferred from electronic annotation /// 5524 // ATP binding // inferred from electronic annotation /// 16874 // ligase activity // inferred from electronic annotation /// 42242 // cobyrinic acid a,c-diamide synthase activity // inferred from electronic annotation
AFFX-BioDn-5_at Sus scrofa Dec 19, 2005 Control AFFX-BioDn-5 dethiobiotin synthetase bioD 9102 // biotin biosynthesis // inferred from electronic annotation /// 9236 // cobalamin biosynthesis // inferred from electronic annotation 166 // nucleotide binding // inferred from electronic annotation /// 287 // magnesium ion binding // inferred from electronic annotation /// 4141 // dethiobiotin synthase activity // inferred from electronic annotation /// 5524 // ATP binding // inferred from electronic annotation /// 16874 // ligase activity // inferred from electronic annotation /// 42242 // cobyrinic acid a,c-diamide synthase activity // inferred from electronic annotation
AFFX-CreX-3_at Sus scrofa Dec 19, 2005 Control AFFX-CreX-3
AFFX-CreX-5_at Sus scrofa Dec 19, 2005 Control AFFX-CreX-5
AFFX-DapX-3_at Sus scrofa Dec 19, 2005 Control AFFX-DapX-3
AFFX-DapX-5_at Sus scrofa Dec 19, 2005 Control AFFX-DapX-5
AFFX-DapX-M_at Sus scrofa Dec 19, 2005 Control AFFX-DapX-M
AFFX-LysX-3_at Sus scrofa Dec 19, 2005 Control AFFX-LysX-3
AFFX-LysX-5_at Sus scrofa Dec 19, 2005 Control AFFX-LysX-5
AFFX-LysX-M_at Sus scrofa Dec 19, 2005 Control AFFX-LysX-M
AFFX-PheX-3_at Sus scrofa Dec 19, 2005 Control AFFX-PheX-3
AFFX-PheX-5_at Sus scrofa Dec 19, 2005 Control AFFX-PheX-5
AFFX-PheX-M_at Sus scrofa Dec 19, 2005 Control AFFX-PheX-M
AFFX-r2-Bs-dap-3_at Sus scrofa Dec 19, 2005 Control AFFX-r2-Bs-dap-3
AFFX-r2-Bs-dap-5_at Sus scrofa Dec 19, 2005 Control AFFX-r2-Bs-dap-5

Total number of rows: 24123

Table truncated, full table size 4528 Kbytes.






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