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Sample GSM63374 Query DataSets for GSM63374
Status Public on Jan 01, 2006
Title cDNA array 0wt/+3wt set1
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
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 2491 1636 1.52269131 0.606623499
CM001A02 1969 1567 1.256524388 0.329438673
CM001A03 1415 1484 0.95349409 -0.068704099
CM001A04 1399 3798 0.368339173 -1.440893259
CM001A05 1262 1321 0.955331986 -0.065925926
CM001A06 196 123 1.595614621 0.674112248
CM001A07 1 11 0.133437991 -2.905758626
CM001A08 1228 1251 0.982122844 -0.026024607
CM001A09 1193 1123 1.062720528 0.087762249
CM001A10 1898 2018 0.940459478 -0.088562312
CM001A11 411 318 1.293861586 0.37168329
CM001A12 556 388 1.432343831 0.51837785
CM001B01 1236 810 1.525517441 0.609298674
CM001B02 198 191 1.037203743 0.052699317
CM001B03 2764 1868 1.480126953 0.565720924
CM001B04 1132 1327 0.852750057 -0.229805149
CM001B05 2062 1412 1.459885352 0.545855076
CM001B06 270 216 1.253084531 0.32548374
CM001B07 4277 10352 0.413169528 -1.275194238
CM001B08 944 1004 0.940046266 -0.089196332

Total number of rows: 11706

Table truncated, full table size 482 Kbytes.




Supplementary data files not provided

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