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Sample GSM1621416 Query DataSets for GSM1621416
Status Public on Mar 19, 2015
Title 125AA-EL36_water_stress-2010_46
Sample type RNA
 
Source name berry
Organism Vitis vinifera
Characteristics tissue: berry
scion cultivar: pinot noir
rootstock: 125AA
developmental stage: EL36
treatment: water stress
year: 2010
Treatment protocol Two water conditions were established for the vines grafted on the two rootstocks: control (C) and water stress treatment (S). To impose water stress, half the rows of the vineyard chosen were covered with a removable plastic film from flowering onwards, covering completely the width of the inter-row on both sides of the plants during rainy days. Water stress was applied to the upper part of the vineyard (slope with 6-7% of inclination) and the control was situated at the lower part.
Growth protocol Grape berries from Pinot noir (Vitis vinifera) grafted on rootstocks Richter 110 (V. rupestris x V. berlandieri) and Kober 125AA (V. riparia x V. berlandieri), were sampled from field-grown vines at two different developmental stages (E-L 35 and E-L 36) according to the modified Eichhorn and Lorenz developmental scale24, during two growing seasons (2009 and 2010). Vines were trained using a vertical shoot positioning system. The experimental vineyard belongs to the University of Geisenheim (49°59’N, 7°57’W, Germany). Twenty rows of Pinot noir were selected, with an average of 17 plants per row.
Extracted molecule total RNA
Extraction protocol Total RNA from berries of Pinot noir grafted onto 110R and 125AA was extracted as described by Reid et al., 2006 (Reid KE, Olsson N, Schlosser J, Peng F, Lund ST. An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biology 2006; 6: 27.). Seeds of each berry were removed before grinding in liquid nitrogen. Total RNA was subjected to DNA digestion with 5 units of RNase-free DNase I (Promega) for 1 h at 37°C. RNA integrity was measured at 260 nm with a micro-spectrophotometer (NanoDrop 200C, NanoDrop products, Wilmington, USA) and visualized by electrophoresis on 1.2% agarose gels. RNA quality was also confirmed using a lab-on-chip (2100 Bioanalyzer, Agilent Technologies, Santa Clara, USA).
Label Cy3
Label protocol Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).
 
Hybridization protocol Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).
Scan protocol Labelling, hybridization and scanning were done by Genotoul Biopuces plateform (Toulouse, France).
Data processing Data were RMA normalized using R/Bioconductor.
 
Submission date Feb 27, 2015
Last update date Mar 20, 2015
Contact name Christian Kappel
E-mail(s) christian.kappel@uni-potsdam.de
Phone +49-331-9775580
Organization name Universität Potsdam
Department Institut für Biochemie und Biologie
Street address Karl-Liebknecht-Str. 24-25, Haus 26
City Potsdam
ZIP/Postal code 14476
Country Germany
 
Platform ID GPL17894
Series (1)
GSE66391 Water limitation and rootstock genotype interact to alter grape berry metabolism through transcriptome reprogramming

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensities

Data table
ID_REF VALUE
CHR10_GSVIVT00006725001_T01 7.692121368
CHR10_GSVIVT00007268001_T01 7.654869976
CHR10_GSVIVT00021093001_T01 8.329214777
CHR10_GSVIVT00021115001_T01 5.877133196
CHR10_GSVIVT00021131001_T01 9.41511119
CHR10_GSVIVT00021157001_T01 8.840541595
CHR10_GSVIVT00021158001_T01 8.853342717
CHR10_GSVIVT00021206001_T01 7.287625075
CHR10_GSVIVT00021217001_T01 8.755689096
CHR10_GSVIVT00021273001_T01 7.355484472
CHR10_GSVIVT00021290001_T01 6.026399115
CHR10_GSVIVT00021333001_T01 5.17782113
CHR10_GSVIVT00021341001_T01 8.129367946
CHR10_GSVIVT00021361001_T01 5.813186379
CHR10_GSVIVT00021408001_T01 5.234682257
CHR10_GSVIVT00021438001_T01 13.23643034
CHR10_GSVIVT00021476001_T01 5.163258155
CHR10_GSVIVT00021483001_T01 5.623653104
CHR10_GSVIVT00021487001_T01 5.226778088
CHR10_GSVIVT00021498001_T01 6.015704313

Total number of rows: 28811

Table truncated, full table size 909 Kbytes.




Supplementary file Size Download File type/resource
GSM1621416_551693A11_2012-12-13_13-38_46_2012-12-13T160925_532.pair.gz 2.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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