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Platform GPL8560 Query DataSets for GPL8560
Status Public on Dec 01, 2009
Title University of Arizona Vitis buds cDNA array
Technology type spotted DNA/cDNA
Distribution non-commercial
Organisms Vitis vinifera; Vitis riparia
Manufacturer Galbraith lab, University of Arizona, Tucson, AZ, USA
Manufacture protocol A total of 7920 cDNA inserts were amplified from the plasmids making up the previously described Vinifera bud EST collection (Keilin et al. 2007). Another 1141 cDNAs were amplified from a Vitis riparia clone collection that was recently described by Mathiason et al. (2008). The PCR products were purified, transferred to 384-well microplates, dried, and resuspended in 3X SSC. A total 9061 PCR products were spotted onto amino-silane-coated slides ("Superamine", Telechem, Sunnyvale, CA). A single array element was printed per clone onto each slide using SMP3 printing pins (Telechem) and a 32-pin head robotic system (‘OmniGrid 100’, GeneMachines, San Carlos, CA) at constant relative humidity (30%). The microarrays contained 9216 spots (including 152 blank spots). Spot diameter was 110 microM, spot spacing was 230 microM and subarray spacing was 460 microM. Slides included 32 grids of 18 columns and 18 rows (rows 17-18 were left empty). The arrays were allowed to air-dry for 10 min and the cDNA spots were immobilized. The quality of the printing process was assessed by hybridization of the first and last array at every print run with Cy3-labeled random 9-mer as described in http://ag.arizona.edu/microarray/Microarraymethod1
 
Description References:

Keilin T, Pang X, Venkateswari J, Halaly T, Crane O, Keren A, Ogrodovitch A, Ophir R, Volpin H, Galbraith D, Or E. Digital expression profiling of a grape-bud EST collection leads to new insight into molecular events during grape-bud dormancy release. Plant Science. 2007 Oct;173(4):446-457.

Mathiason K, He D, Grimplet J, Venkateswari J, Galbraith DW, Or E, Fennell A. Transcript profiling in Vitis riparia during chilling requirement fulfillment reveals coordination of gene expression patterns with optimized bud break. Funct Integr Genomics. 2009 Feb;9(1):81-96. Epub 2008 Jul 17.
 
Contributor(s) Or E
Submission date May 18, 2009
Last update date Dec 01, 2009
Contact name Ron Ophir
Organization name Agricultire Research Organization
Department Fruit Tree Sciences
Lab Genomics lab
Street address POB 6
City Bet-Dagan
ZIP/Postal code 50250
Country Israel
 
Samples (66) GSM404717, GSM404718, GSM404719, GSM404720, GSM404721, GSM404722 
Series (1)
GSE16173 Gene expression profiling of grape-bud response to two alternative dormancy-release stimuli.

Data table header descriptions
ID
Block Block number of printing layout
Row Row number within a block
Column Column number within a block
GB_LIST GenBank accessions of clones
Clone cDNA library Clone identifier. Described in Keilin et al. 2007.
NR_annotation Hit description of blast against NR
Seq_ID Contig ID or Clone ID for singletones
GI GI number from blast run against NR
Pathway Literature-based classification code
Pathway_Description Literature-based classification description
SPOT_ID

Data table
ID Block Row Column GB_LIST Clone NR_annotation Seq_ID GI Pathway Pathway_Description SPOT_ID
10101 1 1 1 EV228251 VV_PEa2a4 VV_PEa2a4 NA
10102 1 1 2 EV228261 VV_PEa2a8 VV_PEa2a8 NA
10103 1 1 3 EV228270 VV_PEa2a12 VV_PEa2a12 NA
10104 1 1 4 EV228359 VV_PEa2e4 VV_PEa2e4 NA
10105 1 1 5 EV228324 VV_PEa2e8 hypothetical protein [Neurospora crassa]gi|28924013|gb|EAA33172.1| hypothetical protein [Neurospora crassa] VV_PEa2e8 32411497 NA
10106 1 1 6 EV228376 VV_PEa2e12 VV_PEa2e12 NA
10107 1 1 7 EV228716 VV_PEa4a4 VV_PEa4a4 NA
10108 1 1 8 EV228704 VV_PEa4a8 putative aldolase [Arabidopsis thaliana]gi|4262250|gb|AAD14543.1| putative aldolase [Arabidopsis thaliana]gi|11762176|gb|AAG40366.1| At2g01140 [Arabidopsis thaliana]gi|15226185|ref|NP_178224.1| fructose-bisphosphate aldolase, putative [Arabidopsis t VV_PEa4a8 2159233 NA
10109 1 1 9 EV228692 VV_PEa4a12 pyruvate decarboxylase [Pisum sativum]gi|1706326|sp|P51850|PDC1_PEA Pyruvate decarboxylase isozyme 1 (PDC)gi|2146786|pir||S65470 pyruvate decarboxylase (EC 4.1.1.1) (clone PDC1) - garden pea VC_grape_1212 117763 NA
10110 1 1 10 EV228775 VV_PEa4e4 VV_PEa4e4 NA
10111 1 1 11 EV228783 VV_PEa4e8 signal peptidase, putative [Arabidopsis thaliana]gi|7523697|gb|AAF63136.1| putative signal peptidase [Arabidopsis thaliana]gi|25406944|pir||E86203 probable signal peptidase [imported] - Arabidopsis thaliana grape_merged_1738 15222236 NA
10112 1 1 12 EV228790 VV_PEa4e12 unknown protein [Arabidopsis thaliana]gi|20268740|gb|AAM14073.1| unknown protein [Arabidopsis thaliana]gi|26451659|dbj|BAC42926.1| unknown protein [Arabidopsis thaliana]gi|30689119|ref|NP_850375.1| ribosomal protein L1 family protein [Arabidopsis thali grape_merged_2077 2128899 NA
10113 1 1 13 EV229167 VV_PEa6a4 TATA-binding protein-associated phosphoprotein Dr1 - Arabidopsis thaliana VV_PEa6a4 2129748 NA
10114 1 1 14 EV229183 VV_PEa6a8 CTR1-like protein kinase [Rosa hybrid cultivar] VV_PEa6a8 13936371 HR Hormone related
10115 1 1 15 EV229118 VV_PEa6a12 LEDI-5c protein [Lithospermum erythrorhizon] VC_grape_2285 4645459 HR Hormone related
10116 1 1 16 EV229327 VV_PEa6e4 VV_PEa6e4 NA
10117 1 1 17 EV229342 VV_PEa6e8 At1g72280 [Arabidopsis thaliana]gi|15218421|ref|NP_177372.1| endoplasmic reticulum oxidoreductin 1 (ERO1) family protein [Arabidopsis thaliana]gi|12323665|gb|AAG51798.1| disulfide bond formation protein, putative; 78451-75984 [Arabidopsis thaliana]g VC_grape_2199 31711714 TR Translation and post translation modification
10118 1 1 18 EV229358 VV_PEa6e12 glutathione S-transferase/peroxidase [Capsicum chinense] grape_merged_2407 58578272 SO Oxidative stress
10201 1 2 1 EV229671 VV_PEa8a4 pathogenesis-related protein 10 [Vitis vinifera] grape_merged_1050 11182124 NA
10202 1 2 2 EV229824 VV_PEa8a8 26S proteasome regulatory subunit S5A [Mesembryanthemum crystallinum]gi|7484606|pir||T12317 26S proteasome regulatory subunit S5A - common ice plant VV_PEa8a8 32242 NA

Total number of rows: 10368

Table truncated, full table size 1478 Kbytes.




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