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Sample GSM63391 Query DataSets for GSM63391
Status Public on Jan 01, 2006
Title cDNA array +3wt/+3fl set1
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 1626 1316 0.809563634 -0.304783609
CM001A02 873 487 0.558150763 -0.841273232
CM001A03 1693 1076 0.635940104 -0.653037202
CM001A04 4357 685 0.157122222 -2.670040856
CM001A05 1611 1941 1.204999792 0.269032898
CM001A06 302 302 1 0
CM001A07 188 188 1 0
CM001A08 1014 1762 1.737774805 0.797241138
CM001A09 1707 1720 1.007734809 0.011116035
CM001A10 2020 1381 0.683579045 -0.548819923
CM001A11 339 580 1.7082717 0.772537454
CM001A12 498 519 1.041424839 0.058558723
CM001B01 511 627 1.226506166 0.294554487
CM001B02 374 472 1.262492307 0.336274597
CM001B03 904 907 1.004040931 0.005818084
CM001B04 844 804 0.951962874 -0.071022784
CM001B05 1120 1448 1.292982504 0.370702753
CM001B06 376 598 1.590859676 0.669806586
CM001B07 4817 1397 0.290141067 -1.785173586
CM001B08 1465 1752 1.195488903 0.257600739

Total number of rows: 11706

Table truncated, full table size 455 Kbytes.




Supplementary data files not provided

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