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Platform GPL3213 Query DataSets for GPL3213
Status Public on Dec 01, 2005
Title [Chicken] Affymetrix Chicken Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Gallus gallus
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

Sequence information for the GeneChip Chicken Genome Array can be used to study gene expression of 33,457 chicken and viral transcripts. Species covered include Gallus gallus (chicken) and 17 avian viruses. Sequence information for this array includes public content from GenBank®, UniGene (Build 18; 15 May 2004), and Ensembl (version 1, released May 2004). Probe sets on the array were designed with 11 oligonucleotide pairs to detect each transcript.
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=chicken
http://www.affymetrix.com/analysis/index.affx
Submission date Nov 30, 2005
Last update date Jun 03, 2009
Organization Affymetrix, Inc.
E-mail 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 (1613) GSM85520, GSM85521, GSM85526, GSM85527, GSM115434, GSM115435 
Series (132)
GSE3702 Early gene expression responses to a Salmonella infection in the chicken intestine
GSE5114 Gene expression in Histone H1 variant deletion chicken DT40 mutant cell
GSE6543 Chick myopia
Relations
Alternative to GPL10234 (Alternative CDF)

Data table header descriptions
ID Affymetrix Probe Set ID
GB_ACC GenBank Accession Number
SPOT_ID
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.
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.
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.
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_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type Sequence Source Target Description 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
AB112960.CDS1.S1_at AB112960.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian leukosis virus AB112960.CDS1 /GEN=env /DB_XREF=GI:32188035 /SEG=AB112960:+383,6898 /DEF=Avian leukosis virus genomic RNA, complete genome. envelope protein /REP_ORG=Avian leukosis virus
AF004856.CDS1.S1_s_at AF004856.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF004856.CDS1 /DB_XREF=GI:2213895 /SEG=AF004856:+31,1134 /DEF=Avian reovirus strain 1733 segment S3, sigma B protein gene, complete cds. sigma B protein /REP_ORG=Avian orthoreovirus
AF004857.CDS1.S1_s_at AF004857.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF004857.CDS1 /DB_XREF=GI:2213897 /SEG=AF004857:+25,321 /DEF=Avian reovirus strain 1733 segment S1, 10 kDa protein, 17 kDa protein and sigma C protein genes, complete cds. 10 kDa protein /REP_ORG=Avian orthoreovirus
AF004857.CDS2.S1_s_at AF004857.CDS2 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF004857.CDS2 /DB_XREF=GI:2213898 /SEG=AF004857:+293,733 /DEF=Avian reovirus strain 1733 segment S1, 10 kDa protein, 17 kDa protein and sigma C protein genes, complete cds. 17 kDa protein /REP_ORG=Avian orthoreovirus
AF004857.CDS3.S1_s_at AF004857.CDS3 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF004857.CDS3 /DB_XREF=GI:2213899 /SEG=AF004857:+630,1610 /DEF=Avian reovirus strain 1733 segment S1, 10 kDa protein, 17 kDa protein and sigma C protein genes, complete cds. sigma C protein /NOTE=Minor outer capsid protein /REP_ORG=Avian orthoreovirus
AF059716.CDS1.S1_at AF059716.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF059716.CDS1 /DB_XREF=GI:3170619 /SEG=AF059716:+16,1266 /DEF=Avian orthoreovirus strain 176 segment S2 major inner capsid protein sigma 1 gene, complete cds. major inner capsid protein sigma 1 /REP_ORG=Avian orthoreovirus
AF059717.CDS1.S1_at AF059717.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF059717.CDS1 /DB_XREF=GI:3170621 /SEG=AF059717:+16,1266 /DEF=Avian orthoreovirus strain 138 segment S2 major inner capsid protein sigma 1 gene, complete cds. major inner capsid protein sigma 1 /REP_ORG=Avian orthoreovirus
AF059721.CDS1.S1_at AF059721.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF059721.CDS1 /DB_XREF=GI:3170629 /SEG=AF059721:+31,1134 /DEF=Avian orthoreovirus strain 138 segment S3 major outer capsid protein sigma 2 gene, complete cds. major outer capsid protein sigma 2 /REP_ORG=Avian orthoreovirus
AF059724.CDS1.S1_at AF059724.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF059724.CDS1 /DB_XREF=GI:3170635 /SEG=AF059724:+24,1127 /DEF=Avian orthoreovirus strain 176 segment S4 nonstructural protein sigma NS gene, complete cds. nonstructural protein sigma NS /REP_ORG=Avian orthoreovirus
AF059725.CDS1.S1_at AF059725.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian orthoreovirus AF059725.CDS1 /DB_XREF=GI:3170637 /SEG=AF059725:+24,1127 /DEF=Avian orthoreovirus strain 138 segment S4 nonstructural protein sigma NS gene, complete cds. nonstructural protein sigma NS /REP_ORG=Avian orthoreovirus
AF176590.CDS1.S1_s_at AF176590.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian pneumovirus AF176590.CDS1 /GEN=N /DB_XREF=GI:6224702 /SEG=AF176590:+14,1198 /DEF=Avian pneumovirus strain United States (Colorado) nucleocapsid protein (N) gene, complete cds and viral leader sequence. nucleocapsid protein /REP_ORG=Avian pneumovirus
AF176591.CDS1.S1_s_at AF176591.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian pneumovirus AF176591.CDS1 /GEN=P /DB_XREF=GI:6224704 /SEG=AF176591:+14,898 /DEF=Avian pneumovirus strain United States (Colorado) phosphoprotein (P) gene, complete cds. phosphoprotein /REP_ORG=Avian pneumovirus
AF176592.CDS1.S1_s_at AF176592.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian pneumovirus AF176592.CDS1 /GEN=M2 /DB_XREF=GI:6224706 /SEG=AF176592:+14,568 /DEF=Avian pneumovirus strain United States (Colorado) matrix glycoprotein M2 ORF1 (M2) and matrix glycoprotein M2 ORF2 (M2) genes, complete cds. matrix glycoprotein M2 ORF1 /REP_ORG=Avian pneumovirus
AF176592.CDS2.S1_s_at AF176592.CDS2 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian pneumovirus AF176592.CDS2 /GEN=M2 /DB_XREF=GI:6224707 /SEG=AF176592:+525,740 /DEF=Avian pneumovirus strain United States (Colorado) matrix glycoprotein M2 ORF1 (M2) and matrix glycoprotein M2 ORF2 (M2) genes, complete cds. matrix glycoprotein M2 ORF2 /REP_ORG=Avian pneumovirus
AF218359.CDS1.S1_at AF218359.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian reovirus strain 138 AF218359.CDS1 /DB_XREF=GI:7288542 /SEG=AF218359:+25,321 /DEF=Avian reovirus strain 138 segment S1 membrane fusion protein p10, p17, and virus-cell attachment protein sigma C genes, complete cds. membrane fusion protein p10 /NOTE=type I transmembrane protein /REP_ORG=Avian reovirus strain 138
AF218359.CDS2.S1_at AF218359.CDS2 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian reovirus strain 138 AF218359.CDS2 /DB_XREF=GI:7288543 /SEG=AF218359:+293,733 /DEF=Avian reovirus strain 138 segment S1 membrane fusion protein p10, p17, and virus-cell attachment protein sigma C genes, complete cds. p17 /NOTE=type I transmembrane protein /REP_ORG=Avian reovirus strain 138
AF218359.CDS3.S1_at AF218359.CDS3 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Avian reovirus strain 138 AF218359.CDS3 /DB_XREF=GI:7288544 /SEG=AF218359:+630,1610 /DEF=Avian reovirus strain 138 segment S1 membrane fusion protein p10, p17, and virus-cell attachment protein sigma C genes, complete cds. virus-cell attachment protein sigma C /NOTE=type I transmembrane protein /REP_ORG=Avian reovirus strain 138
AF243438.CDS1.S1_s_at AF243438.CDS1 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Gallid herpesvirus 2 AF243438.CDS1 /GEN=MDV001 /DB_XREF=GI:10180698 /SEG=AF243438:+1517,2176 /DEF=Gallid herpesvirus 2 serotype 1 isolate Md5, complete genome. hypothetical protein /REP_ORG=Gallid herpesvirus 2 telomerase RNA TERC 379037 NR_001594
AF243438.CDS10.S1_s_at AF243438.CDS10 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Gallid herpesvirus 2 AF243438.CDS10 /GEN=MDV008 /DB_XREF=GI:10180700 /SEG=AF243438:+13833,14300 /DEF=Gallid herpesvirus 2 serotype 1 isolate Md5, complete genome. 24kD phosphoprotein pp24 /NOTE=uses alternate N-terminal exon b /REP_ORG=Gallid herpesvirus 2
AF243438.CDS11.S1_s_at AF243438.CDS11 Gallus gallus Mar 11, 2009 Consensus sequence Affymetrix Proprietary Database Gallid herpesvirus 2 AF243438.CDS11 /GEN=MDV010 /DB_XREF=GI:10180702 /SEG=AF243438:+14535,16875 /DEF=Gallid herpesvirus 2 serotype 1 isolate Md5, complete genome. lipase /NOTE=uses alternate N-terminal exon b /REP_ORG=Gallid herpesvirus 2

Total number of rows: 38535

Table truncated, full table size 20754 Kbytes.






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