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Sample GSM881672 Query DataSets for GSM881672
Status Public on Sep 10, 2012
Title Tendril-Y_rep3
Sample type RNA
 
Source name young tendril (pool of tendrils from shoot of 7 leaves), replicate 3
Organism Vitis vinifera
Characteristics cultivar: Corvina
tissue: Tendril
developmental stage: young tendril (pool of tendrils from shoot of 7 leaves)
Growth protocol Vitis vinifera cv. Corvina (clone 48) samples were collected from a 7-year-old vineyard (45° 27’ 17” N, 11° 03’ 14” E, Montorio, Verona province, Italy) during 2008/2009 growing seasons. The vineyard is at 130 m. above sea level (a.s.l.), planted on a soil with the following composition: 36% sand, 36% say and 28% silt. The replacement cane Guyot rows are north-south oriented and 41B in used as rootstock.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from ~100 mg of liquid-nitrogen-grinded tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) following the manufacturer’s protocol. For berry flesh, senescing leaf and woody stem, it was necessary to isolate RNA from ~400 mg of grinded material, while for berry pericarp and skin, seed, rachis, root, latent and winter bud, from ~200 mg. Lithium Chloride precipitation treatment was applied to some of the total RNA samples (from winter bud, from seed and rachis at vèraison and mid-ripening, from woody stem) to remove 230wavelenght-absorbant contaminants. Briefly, LiCl solution was mixed with total RNA solution to a final concentration of 2.5 M; after over-night incubation at 4°C, a cold centrifugation and ethanol-70% washing step, total RNA was resuspended in water.
Label Cy3
Label protocol cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).
 
Hybridization protocol Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).
Scan protocol Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.
Description tendril_04,30_m_364203A02.pair
Data processing Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.
 
Submission date Feb 28, 2012
Last update date Sep 10, 2012
Contact name Alberto Ferrarini
E-mail(s) alberto.ferrarini@univr.it
Phone +39-045-802-7058
Organization name University of Verona
Department Scientific and Technological Department
Lab Plant Functional Genomics Centre
Street address Strada le Grazie, 15
City Verona
State/province Veneto
ZIP/Postal code 37134
Country Italy
 
Platform ID GPL13936
Series (1)
GSE36128 The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program

Data table header descriptions
ID_REF
VALUE Nimblescan v2.5 software calculated RMA-normalized signal intensities.

Data table
ID_REF VALUE
VitusP00000001 82.30
VitusP00000003 44.13
VitusP00000007 4282.34
VitusP00000008 5749.65
VitusP00000011 279.42
VitusP00000015 160.30
VitusP00000017 257.03
VitusP00000018 271.61
VitusP00000021 90.60
VitusP00000024 207.86
VitusP00000027 306.01
VitusP00000030 175.41
VitusP00000031 25.60
VitusP00000034 79.96
VitusP00000038 49.30
VitusP00000040 215.37
VitusP00000043 29.00
VitusP00000045 33.78
VitusP00000048 98.26
VitusP00000050 258.54

Total number of rows: 139363

Table truncated, full table size 2999 Kbytes.




Supplementary file Size Download File type/resource
GSM881672_tendril_04_30_m_364203A02.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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