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Sample GSM63378 Query DataSets for GSM63378
Status Public on Jan 01, 2006
Title cDNA array 0wt/+3wt set3
Sample type RNA
 
Channel 1
Source name 0 DPA wide-type cotton ovule
Organism Gossypium hirsutum
Characteristics Extracted total RNA from 0 DPA wide-type cotton ovules
Extracted molecule total RNA
Label Cy5
 
Channel 2
Source name +3 DPA wide-type cotton ovule
Organism Gossypium hirsutum
Characteristics Extracted total RNA from +3 DPA wide-type cotton ovules
Extracted molecule total RNA
Label Cy3
 
 
Description Comparison of gene expression profiles of 0 DPA and +3 DPA wild-type upland cotton ovules.
Data processing All microarrays were scanned with a ScanArray Express scanner using the ScanArray 2.0 software (Packard Bioscience, Meriden, CT) and analyzed using the GenePix Pro 4.0 software (Axon Instruments, Foster City, CA). We quantified signal intensities of individual spots from the 16-bit TIFF images using GenePix Pro 4.0 (Axon Instruments). Since extensive expression pattern shift was recorded in mRNA populations of late developmental stages, such as the 10dpa/3dpa sample pair shown in Fig. 1C, we applied a linear normalization strategy (van de Peppel et al., 2003) instead of the nonlinear global-intensity-based LOWESS program used for most genome-wide microarrays (Yang et al., 2002). Expression ratios were collected only on those spots with signal intensity >800 in at least one dye channel on the microarray slides. Experimental parameters will be included in supplementary file.
 
Submission date Jul 11, 2005
Last update date Dec 26, 2005
Contact name Yu-Xian Zhu
E-mail(s) zhuyx@water.pku.edu.cn
Phone 86-10-62751193
Fax 86-10-62754427
Organization name College of life sciences, Peking University
Lab National Lab of Protein Engineering & Plant Genetic Engineering
Street address 5# Summer Palace Road
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL2610
Series (1)
GSE2901 cDNA array expression profile of wild-type and fl-mutant upland cotton ovules

Data table header descriptions
ID_REF
Cy5_0wt Signal intensity for 0 DPA wild type sample (Cy5)
Cy3_wt+3 Signal intensity for +3 DPA wild type sample (Cy3)
PRE_VALUE Ratio: 0wt/wt+3
VALUE Log ratio: log2 of PRE_VALUE

Data table
ID_REF Cy5_0wt Cy3_wt+3 PRE_VALUE VALUE
CM001A01 2869 1922 1.49253988 0.57776948
CM001A02 1558 1376 1.132780906 0.179868853
CM001A03 1517 1659 0.914317898 -0.129232233
CM001A04 988 3249 0.30402029 -1.717760482
CM001A05 1364 1493 0.913736959 -0.130149184
CM001A06 73 67 1.085190688 0.117948574
CM001A07 4 2 2.279569892 1.188761643
CM001A08 1014 999 1.014750123 0.021124515
CM001A09 1438 1462 0.983629858 -0.023812567
CM001A10 1677 1773 0.946252072 -0.079703541
CM001A11 310 276 1.123171973 0.167578841
CM001A12 461 345 1.334410535 0.416202584
CM001B01 904 614 1.471394544 0.557184147
CM001B02 343 274 1.254491364 0.32710254
CM001B03 1898 1348 1.407656334 0.493295156
CM001B04 1329 1273 1.043673196 0.061670033
CM001B05 1635 1172 1.394500945 0.479748912
CM001B06 321 253 1.26527883 0.339455347
CM001B07 3297 8994 0.366545145 -1.447937198
CM001B08 1131 1176 0.961112457 -0.057222849

Total number of rows: 11706

Table truncated, full table size 482 Kbytes.




Supplementary data files not provided

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