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Sample GSM1201916 Query DataSets for GSM1201916
Status Public on Aug 07, 2013
Title Rep1_GSHPulp
Sample type RNA
 
Source name GSH berry Class-Pulp
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 LDL4121-34
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 40.46163235
VitusP00000003 8.785858828
VitusP00000007 4671.609414
VitusP00000008 12695.35354
VitusP00000011 267.9968742
VitusP00000015 355.8929853
VitusP00000017 229.8936996
VitusP00000018 256.9787789
VitusP00000021 492.5643345
VitusP00000024 420.7390964
VitusP00000027 411.5175091
VitusP00000030 140.4333027
VitusP00000031 29.27686073
VitusP00000034 117.0593345
VitusP00000038 43.08278997
VitusP00000040 1484.983065
VitusP00000043 16.47043349
VitusP00000045 83.49951091
VitusP00000048 433.6973504
VitusP00000050 906.7691758

Total number of rows: 137604

Table truncated, full table size 3613 Kbytes.




Supplementary file Size Download File type/resource
GSM1201916_Rep1_GSHPulp.pair.gz 2.2 Mb (ftp)(http) PAIR
GSM1201916_Rep1_GSH_Pulp.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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