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Sample GSM1201939 Query DataSets for GSM1201939
Status Public on Aug 07, 2013
Title Rep3_GSHSeed
Sample type RNA
 
Source name GSH berry Class-Seed
Organism Vitis vinifera
Characteristics genotype: Pinot Noir - clone Pommard
Treatment protocol None
Growth protocol Individual berries of Vitis vinifera Pinot Noir clone 48 berries were sampled from one vineyard at three development stages (prevéraison, midvéraison, and harvest)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
Label Cy3
Label protocol Labeling was performed in Deluc's Lab following NimbleGen cDNA synthesis and labeling reactions operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by the Center For Genome Research and Biocomputing, OSU following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by the Center For Genome Research and Biocomputing, OSU following their standard operating protocol. See www.nimblegen.com. Each microarray was scanned using an Axon GenePix 4400A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.
Description LDL4121-57
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS package software (Simon and Biot, 2011)
 
Submission date Aug 06, 2013
Last update date Aug 07, 2013
Contact name Laurent Gerard Deluc
E-mail(s) delucl@hort.oregonstate.edu
Phone 541-737-4356
Organization name Oregon State University
Department Horticulture
Lab 4121
Street address 4017 ALS Building
City Corvallis
State/province OR
ZIP/Postal code 97331
Country USA
 
Platform ID GPL13936
Series (1)
GSE49569 Plasticity of the ripening process among berry classes

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
VitusP00000001 17.66336053
VitusP00000003 36.87489531
VitusP00000007 2062.069573
VitusP00000008 7142.719017
VitusP00000011 573.7652869
VitusP00000015 657.2835408
VitusP00000017 446.6542551
VitusP00000018 475.2754456
VitusP00000021 1169.84989
VitusP00000024 781.2611599
VitusP00000027 1205.149414
VitusP00000030 1041.935208
VitusP00000031 133.35989
VitusP00000034 99.08965295
VitusP00000038 59.31689103
VitusP00000040 702.0243345
VitusP00000043 121.7025885
VitusP00000045 307.3662392
VitusP00000048 1147.664969
VitusP00000050 1654.230525

Total number of rows: 137604

Table truncated, full table size 3614 Kbytes.




Supplementary file Size Download File type/resource
GSM1201939_Rep3_GSHSeed.pair.gz 2.2 Mb (ftp)(http) PAIR
GSM1201939_Rep3_GSH_Seed.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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