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Sample GSM1201900 Query DataSets for GSM1201900
Status Public on Aug 07, 2013
Title Rep3_PSHSkin
Sample type RNA
 
Source name PSH berry Class-Skin
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 LDL4121-18
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 22.35186253
VitusP00000003 11.44750684
VitusP00000007 2806.194176
VitusP00000008 11320.97211
VitusP00000011 341.5459218
VitusP00000015 446.3842551
VitusP00000017 277.4052075
VitusP00000018 315.8517154
VitusP00000021 325.1844932
VitusP00000024 95.60695652
VitusP00000027 238.5252869
VitusP00000030 241.3202075
VitusP00000031 46.32981951
VitusP00000034 171.5152869
VitusP00000038 85.57089775
VitusP00000040 735.1161599
VitusP00000043 167.4603662
VitusP00000045 271.5180646
VitusP00000048 1751.461954
VitusP00000050 1494.857509

Total number of rows: 137604

Table truncated, full table size 3613 Kbytes.




Supplementary file Size Download File type/resource
GSM1201900_Rep3_PSHSkin.pair.gz 2.2 Mb (ftp)(http) PAIR
GSM1201900_Rep3_PSH_Skin.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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