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Platform GPL1320 Query DataSets for GPL1320
Status Public on Jul 01, 2004
Title [Vitis_Vinifera] Affymetrix Vitis vinifera (Grape) Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Vitis vinifera
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 GeneChipĀ® Vitis vinifera Genome Array is the first array to provide comprehensive coverage of the V. vinifera genome.

14,000 V. vinifera transcripts and 1,700 transcripts from other Vitis species can be interrogated.

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Sixteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChipĀ® Vitis vinifera (Grape) Genome Array. Sequences used in the design of the V. vinifera Genome Array were selected from GenBankĀ®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 7, Oct 2003).

Annotations derived from Affymetrix CSV file dated 6/23/2004
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=grape
http://www.affymetrix.com/analysis/index.affx
Submission date Jul 01, 2004
Last update date Jun 22, 2017
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 (1019) GSM147672, GSM147673, GSM147674, GSM147675, GSM147676, GSM147677 
Series (35)
GSE6404 V. vinifera 'Cabernet sauvignon' and V. aestivalis 'Norton' innoculated with Erysiphe necator conidiospores
GSE7394 Gene expression analysis in grape berries at veraison (SIB-05)
GSE7677 Grape berry developmental series from a vineyard in Willunga, South Australia (WIL-04)

Data table header descriptions
ID Affymetrix Probe Set ID
GB_ACC GenBank Accession Number
SPOT_ID Column added by GEO staff to facilitate sequence tracking in Entrez GEO
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 Cluster identification number with a sub-cluster identifier appended.
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.

Data table
ID GB_ACC SPOT_ID Sequence Type Sequence Source Transcript ID Target Description Representative Public ID
1606368_s_at CF208516 Consensus sequence GenBank Vvi.7514.1 gb:CF208516 /DB_XREF=gi:33402889 /DB_XREF=CAB20003_IIa_Ra_F12 /CLONE=CAB20003_IIa_Ra_F12 /TID=Vvi.7514.1 /CNT=108 /FEA=mRNA /TIER=Stack /STK=32 /UG=Vvi.7514 /UG_TITLE=Vitis vinifera actin 2 (act2) mRNA, partial cds /REP_ORG=V. vinifera CF208516
1606427_at CF414075 Consensus sequence GenBank Vvi.11550.1 gb:CF414075 /DB_XREF=gi:34415321 /DB_XREF=CSECS032D02_POSn0036 /CLONE=CSECS032D02 /TID=Vvi.11550.1 /CNT=1 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Vvi.11550 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_174029.1 (A.thaliana) unknown protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CF414075
1606428_at CK138206.1 Consensus sequence GenBank VviAffx.29897.1 gb:CK138206.1 /DB_XREF=gi:38654632 /TID=VviAffx.29897.1 /CNT=1 /FEA=mRNA /TIER=ConsEnd /STK=0 /NOTE=sequence(s) not in UniGene /DEF=VRJ219 Vitis riparia endodormant bud - VRJ Vitis riparia cDNA clone VRJ219 3, mRNA sequence. /REP_ORG=V. riparia CK138206.1
1606429_at CF373019 Consensus sequence GenBank Vvi.10710.1 gb:CF373019 /DB_XREF=gi:34320265 /DB_XREF=CSECS082H08_FLOn0012 /CLONE=CSECS082H08 /TID=Vvi.10710.1 /CNT=1 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Vvi.10710 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_201042.1 (A.thaliana) DC1.2 homologue - like protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CF373019
1606430_at CF510781 Consensus sequence GenBank Vvi.12732.2 gb:CF510781 /DB_XREF=gi:34542549 /DB_XREF=CAbud0001_IIR_H04 /CLONE=CAbud0001_IIR_H04 /TID=Vvi.12732.2 /CNT=2 /FEA=EST /TIER=ConsEnd /STK=0 /UG=Vvi.12732 /UG_TITLE=Vitis vinifera transcribed sequence with moderate similarity to protein ref:NP_173115.1 (A.thaliana) unknown protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CF510781
1606431_at BQ796467 Consensus sequence GenBank Vvi.6723.1 gb:BQ796467 /DB_XREF=gi:22011433 /DB_XREF=EST /CLONE=RT041H01 /TID=Vvi.6723.1 /CNT=7 /FEA=EST /TIER=ConsEnd /STK=2 /UG=Vvi.6723 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_194229.1 (A.thaliana) geranylgeranylated protein ATGP4 (Arabidopsis thaliana) /REP_ORG=V. vinifera BQ796467
1606432_at CD013716 Consensus sequence GenBank Vvi.8994.2 gb:CD013716 /DB_XREF=gi:30330454 /DB_XREF=VVD001G01_397039 /CLONE=VVD001G01 (5) /TID=Vvi.8994.2 /CNT=7 /FEA=EST /TIER=ConsEnd /STK=0 /UG=Vvi.8994 /UG_TITLE=Vitis vinifera transcribed sequence with moderate similarity to protein ref:NP_568066.1 (A.thaliana) putative protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CD013716
1606433_at CB342242 Consensus sequence GenBank Vvi.1185.1 gb:CB342242 /DB_XREF=gi:28963209 /DB_XREF=CA32EN0002_IaR_D09 /CLONE=CA32EN0002_IaR_D09 /TID=Vvi.1185.1 /CNT=20 /FEA=EST /TIER=ConsEnd /STK=2 /UG=Vvi.1185 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_564411.1 (A.thaliana) expressed protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CB342242
1606434_at CB918530 Consensus sequence GenBank Vvi.3205.2 gb:CB918530 /DB_XREF=gi:30133191 /DB_XREF=VVD034E11_347693 /CLONE=VVD034E11 (5) /TID=Vvi.3205.2 /CNT=6 /FEA=EST /TIER=ConsEnd /STK=0 /UG=Vvi.3205 /UG_TITLE=Vitis vinifera transcribed sequence with strong similarity to protein ref:NP_199088.1 (A.thaliana) P34795) (Arabidopsis thaliana) /REP_ORG=V. vinifera CB918530
1606435_at CF204110.1 Consensus sequence GenBank VviAffx.28180.1 gb:CF204110.1 /DB_XREF=gi:33398483 /TID=VviAffx.28180.1 /CNT=1 /FEA=mRNA /TIER=ConsEnd /STK=0 /NOTE=sequence(s) not in UniGene /DEF=RR890915I0002_IIIa_Ra_C08 Vitis sp. RR890915I Vitis hybrid cultivar cDNA clone RR890915I0002_IIIa_Ra_C08 3, mRNA sequence. /REP_ORG=V. hybrid cultivar CF204110.1
1606436_s_at CB007992 Consensus sequence GenBank Vvi.7636.2 gb:CB007992 /DB_XREF=gi:27585297 /DB_XREF=VVC052F05_147444 /CLONE=VVC052F05 (5) /TID=Vvi.7636.2 /CNT=83 /FEA=EST /TIER=Stack /STK=6 /UG=Vvi.7636 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_194534.1 (A.thaliana) senescence-associated protein -like (Arabidopsis thaliana) /REP_ORG=V. vinifera CB007992
1606437_at CA814156 Consensus sequence GenBank Vvi.7968.1 gb:CA814156 /DB_XREF=gi:26263093 /DB_XREF=CA48LN08IR-C1 /CLONE=CA48LN08IR-C1 /TID=Vvi.7968.1 /CNT=14 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Vvi.7968 /UG_TITLE=Vitis vinifera transcribed sequence with moderate similarity to protein ref:NP_200007.1 (A.thaliana) DNA-directed RNA polymerase II subunit-like protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CA814156
1606438_at CF215256 Consensus sequence GenBank Vvi.2347.1 gb:CF215256 /DB_XREF=gi:33409629 /DB_XREF=CAST0001_IR_E08 /CLONE=CAST0001_IR_E08 /TID=Vvi.2347.1 /CNT=5 /FEA=EST /TIER=ConsEnd /STK=3 /UG=Vvi.2347 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_177673.1 (A.thaliana) hypothetical protein (Arabidopsis thaliana) /REP_ORG=V. vinifera CF215256
1606439_s_at CF513904 Consensus sequence GenBank Vvi.12361.1 gb:CF513904 /DB_XREF=gi:34545672 /DB_XREF=CAbud0007_IIIR_B06 /CLONE=CAbud0007_IIIR_B06 /TID=Vvi.12361.1 /CNT=7 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Vvi.12361 /UG_TITLE=Vitis vinifera transcribed sequence with weak similarity to protein ref:NP_565597.1 (A.thaliana) F-box protein family, AtFBL6 (Arabidopsis thaliana) /REP_ORG=V. vinifera CF513904
1606440_at CB977937 Consensus sequence GenBank Vvi.6188.1 gb:CB977937 /DB_XREF=gi:30301143 /DB_XREF=CAB40005_IIIa_Ra_A07 /CLONE=CAB40005_IIIa_Ra_A07 /TID=Vvi.6188.1 /CNT=2 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Vvi.6188 /UG_TITLE=Vitis vinifera transcribed sequences /REP_ORG=V. vinifera CB977937
1606441_at CD011013 Consensus sequence GenBank VviAffx.19145.1 gb:CD011013 /DB_XREF=gi:30327751 /DB_XREF=VVB118B12_382899 /CLONE=VVB118B12 (5) /TID=VviAffx.19145.1 /CNT=9 /FEA=EST /TIER=ConsEnd /STK=0 /NOTE=sequence(s) not in UniGene /REP_ORG=V. vinifera CD011013
1606442_at CF511173 Consensus sequence GenBank Vvi.3277.1 gb:CF511173 /DB_XREF=gi:34542941 /DB_XREF=CAbud0002_IF_D04 /CLONE=CAbud0002_IF_D04 /TID=Vvi.3277.1 /CNT=25 /FEA=EST /TIER=ConsEnd /STK=0 /UG=Vvi.3277 /UG_TITLE=Vitis vinifera transcribed sequence with moderate similarity to protein sp:Q9ZSK3 (A.thaliana) ADF4_ARATH Actin-depolymerizing factor 4 (ADF-4) (AtADF4) /REP_ORG=V. vinifera CF511173
1606443_at CF207585 Consensus sequence GenBank Vvi.9302.1 gb:CF207585 /DB_XREF=gi:33401958 /DB_XREF=CAB20001_Ia_Ra_G01 /CLONE=CAB20001_Ia_Ra_G01 /TID=Vvi.9302.1 /CNT=1 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Vvi.9302 /UG_TITLE=Vitis vinifera transcribed sequence /REP_ORG=V. vinifera CF207585
1606444_at CB972596 Consensus sequence GenBank Vvi.5190.1 gb:CB972596 /DB_XREF=gi:30295802 /DB_XREF=CAB30001_IIa_Ra_C05 /CLONE=CAB30001_IIa_Ra_C05 /TID=Vvi.5190.1 /CNT=5 /FEA=EST /TIER=ConsEnd /STK=4 /UG=Vvi.5190 /UG_TITLE=Vitis vinifera transcribed sequence with moderate similarity to protein ref:NP_187982.1 (A.thaliana) protein kinase, putative (Arabidopsis thaliana) /REP_ORG=V. vinifera CB972596
1606445_a_at CF512668 Consensus sequence GenBank Vvi.7648.2 gb:CF512668 /DB_XREF=gi:34544436 /DB_XREF=CAbud0004_IIF_A11 /CLONE=CAbud0004_IIF_A11 /TID=Vvi.7648.2 /CNT=4 /FEA=EST /TIER=ConsEnd /STK=0 /UG=Vvi.7648 /UG_TITLE=Vitis vinifera transcribed sequence with moderate similarity to protein ref:NP_192237.1 (A.thaliana) putative component of cytochrome B6-F complex (Arabidopsis thaliana) /REP_ORG=V. vinifera CF512668

Total number of rows: 16602

Table truncated, full table size 5589 Kbytes.




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