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Sample GSM2038581 Query DataSets for GSM2038581
Status Public on Jun 26, 2017
Title 5vs1-R2
Sample type RNA
 
Channel 1
Source name berry skins, stage 1
Organism Vitis vinifera
Characteristics cultivar: Moscato Bianco
tissue: berry skins
developmental stage: 1 (pre-veraison, 4.4 °Brix)
Growth protocol Berries of the cultivar Moscato Bianco (Vitis vinifera L.) were sampled in 2006 from pre-véraison to over-ripening, for a total of 13 collection dates. At each time point, ten bunches were taken from ten plants out of the ~250 grown in the experimental field “Inferno” of FEM (Fondazione Edmund Mach, San Michele all’Adige, Italy). Care was paid to sample from different vines and positions within each vine. In the lab, berries were pooled in order to minimize environmental effects. Berries were hand-peeled, the skins were immediately frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Five of the 13 time points were used for microarray analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from grape skins using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, St. Louis, Missouri, USA). RNA quantity and quality were evaluated with a NanoDrop ND-8000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, Ontario, Canada).
Label Cy3
Label protocol Fluorescently (Cy3/Cy5) labelled antisense RNA (aRNA) targets were obtained using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Austin, Texas, USA) according to manufacturer’s instructions. Six hundred pmol Cy3- and Cy5-labelled aRNA were pooled together, fragmented and adjusted to 100 µL with hybridization buffer.
 
Channel 2
Source name berry skins, stage 5
Organism Vitis vinifera
Characteristics cultivar: Moscato Bianco
tissue: berry skins
developmental stage: 5 (over-ripening, 19.0 °Brix)
Growth protocol Berries of the cultivar Moscato Bianco (Vitis vinifera L.) were sampled in 2006 from pre-véraison to over-ripening, for a total of 13 collection dates. At each time point, ten bunches were taken from ten plants out of the ~250 grown in the experimental field “Inferno” of FEM (Fondazione Edmund Mach, San Michele all’Adige, Italy). Care was paid to sample from different vines and positions within each vine. In the lab, berries were pooled in order to minimize environmental effects. Berries were hand-peeled, the skins were immediately frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Five of the 13 time points were used for microarray analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from grape skins using the SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, St. Louis, Missouri, USA). RNA quantity and quality were evaluated with a NanoDrop ND-8000 spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, Ontario, Canada).
Label Cy5
Label protocol Fluorescently (Cy3/Cy5) labelled antisense RNA (aRNA) targets were obtained using the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion, Austin, Texas, USA) according to manufacturer’s instructions. Six hundred pmol Cy3- and Cy5-labelled aRNA were pooled together, fragmented and adjusted to 100 µL with hybridization buffer.
 
 
Hybridization protocol Just before hybridization, the oligos were fixed on the chip by exposure to 100 MJ of UV light in a UV Stratalinker 2400 crosslinker (Stratagene, La Jolla, California, USA). The slides were then soaked twice in 0.2% sodium dodecyl sulfate (SDS) for 1 min. The probe solution was denatured at 100 °C for 1 min, cooled on ice for 2 min, stabilized at 37 °C for 5 min and injected into the hybridization chamber of the HS 4800 Hybridization Station (Tecan, Durham, North Carolina, USA). The slides were incubated at 37 °C for 16 h with medium agitation and then washed sequentially at 30 °C in 1X saline-sodium citrate (SSC)/0.1% SDS for 1 min 3 times, in 0.1X SSC/0.1% SDS for 1 min 3 times and finally in 0.1X SSC for 30 s.
Scan protocol Washed slides were quickly dried with nitrogen and immediately scanned at 532 (Cy3) and 635 (Cy5) nm with GenePix 4000B fluorescence reader (Molecular Devices, Sunnyvale, California, USA) using GenePix 4.0 software. Parameters were fixed as follows: 400 V at 532 nm and 460 V at 635 nm for PTM (photomultiplier), 100% power, 5 for pixel size and 3 lines to average.
Description Vitis vinifera L.
Data processing Spot intensities were quantified with the software MAIA 2.75 (Novikov and Barillot, 2007). After excluding bad quality spots, median intensity gene expression data without background subtraction were normalized by a global lowess method followed by a print-tip median method with a modified version of the Goulphar script version 1.1.2 (Lemoine et al., 2006).
 
Submission date Jan 13, 2016
Last update date Jun 26, 2017
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 GPL6637
Series (1)
GSE76834 Drawing links from transcriptome to metabolites: the evolution of aroma in the ripening berry of Moscato bianco (Vitis vinifera L.)

Data table header descriptions
ID_REF
VALUE Lowess print tip normalized log2 ratios (Cy5/Cy3) (M-values)

Data table
ID_REF VALUE
100001 0.393
100002 -0.185
100003 -1.401
100004 0.35
100005 -0.297
100006 -0.671
100007 -0.291
100008 0.031
100009 0.76
100010 -0.232
100011 -0.698
100012 -0.257
100013 0.334
100014 -0.773
100015 0.142
100016 -0.441
100017 -0.164
100018 -0.192
100019 0.379
100020 -1.074

Total number of rows: 16416

Table truncated, full table size 213 Kbytes.




Supplementary file Size Download File type/resource
GSM2038581_13-12-07_447-14K-2g_cya3-400_10-cy5-460_res.txt.gz 709.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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