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Sample GSM227149 Query DataSets for GSM227149
Status Public on Sep 30, 2009
Title 17_G
Sample type RNA
 
Source name developing caryopsis from timepoint 21 and BiolRep2_DS
Organism Triticum aestivum
Characteristics RNA Sample ID:10
TimePoint (DPA): 21
BiolRep:BiolRep2_DS
Array ID: 34
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from developing grains using TRIZOL (Invitrogen), treated with RQ1 DNAse (Promega) and was re-purified using RNA Easy columns (QIAGEN).
Label Alexa 555
Label protocol Ten microgram of total RNA was indirectly labeled with Alexa 555 and Alexa 647 fluorophores (Molecular Probes Inc) using the protocol recommended by the manufacturer.
 
Hybridization protocol Hybridization was carried out using the Pronto! Hybridization kit reagents (Corning Inc, NY) following the supplied protocol.
Scan protocol Hybridized slides were scanned using a Genepix 4000B microarray scanner and raw spot fluorescence intensities were collected using GenePix Pro version 5.0.
Description This study looked at 7835 genes in wheat caryopses.
Data processing The logarithms (base 2) of the original intensity values, not the ratios, for each probe obtained from each fluorescent channel were used. To reduce any dye bias introduced during RNA labeling, the global median value of all the signals per channel on each individual array was subtracted from each spot raw intensity signal and divided by the standard deviation. The expression values per gene were centered based on the median value of expression of the gene across all time-points. We used SAS PROC STDIZE to normalize the data set by array and then by gene for all samples.
 
Submission date Sep 05, 2007
Last update date Aug 14, 2011
Contact name Debbie Laudencia-Chingcuanco
Organization name USDA-ARS
Department Western Regional Research Center
Lab Genomics and Gene Discovery Research Unit
Street address 800 Buchanan Street
City Albany
State/province CA
ZIP/Postal code 94710
Country USA
 
Platform ID GPL5808
Series (1)
GSE8963 Transcriptome profiling of wheat caryopsis development

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 1.089119625
2 0.387394744
3 -1.387574546
4 2.455371943
5 0.445396102
6 0.483418372
7 1.469351072
8 0.669499957
9 0.79923785
10 0.443455386
11 3.659253383
12 0.179457818
13 1.068872611
14 0.424456188
15 0.357585593
16 0.584349945
17 0.238187511
18 0.160921987
19 0.646862384
20 3.073711429

Total number of rows: 10283

Table truncated, full table size 171 Kbytes.




Supplementary file Size Download File type/resource
GSM227149.gpr.gz 1017.4 Kb (ftp)(http) GPR
Processed data included within Sample table

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