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Sample GSM63393 Query DataSets for GSM63393
Status Public on Jan 01, 2006
Title cDNA array +3wt/+3fl set2
Sample type RNA
 
Channel 1
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 Cy5
 
Channel 2
Source name +3 DPA fl-mutant cotton ovule
Organism Gossypium hirsutum
Characteristics Extracted total RNA from +3 DPA fl-mutant cotton ovules
Extracted molecule total RNA
Label Cy3
 
 
Description Comparison of gene expression profiles of +3 DPA wt and +3 DPA fl-mutant uplant 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_wt+3 Signal intensity for +3 DPA wild type sample (Cy5)
Cy3_fl+3 Signal intensity for +3 DPA fl-mutant sample (Cy3)
PRE_VALUE Ratio: wt+3/fl+3
VALUE Log ratio: log2 of PRE_VALUE

Data table
ID_REF Cy5_wt+3 Cy3_fl+3 PRE_VALUE VALUE
CM001A01 1308 768 0.587066173 -0.768404965
CM001A02 46 46 1 0
CM001A03 1879 1386 0.7379671 -0.438371596
CM001A04 1191 629 0.528256079 -0.92069063
CM001A05 923 721 0.781396912 -0.355872541
CM001A06 552 552 1 0
CM001A07 320 320 1 0
CM001A08 601 601 1 0
CM001A09 381 381 1 0
CM001A10 271 271 1 0
CM001A11 554 554 1 0
CM001A12 402 402 1 0
CM001B01 607 607 1 0
CM001B02 583 583 1 0
CM001B03 813 956 1.175252252 0.232970445
CM001B04 1709 1391 0.813726411 -0.297384278
CM001B05 995 1633 1.64022362 0.713892518
CM001B06 123 123 1 0
CM001B07 2856 888 0.310876771 -1.685585272
CM001B08 696 839 1.205978506 0.270204195

Total number of rows: 11706

Table truncated, full table size 418 Kbytes.




Supplementary data files not provided

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