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Sample GSM63366 Query DataSets for GSM63366
Status Public on Jan 01, 2006
Title cDNA array +3wt/+3wt set2 (self-to-self)
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 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 Self-to-self hybridizations of genes from +3 DPA wild-type upland cotton ovules to confirm reproducibility of array data.
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 Jul 11, 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_wt+3 Signal intensity for +3 DPA wild type sample (Cy3)
PRE_VALUE Ratio: wt+3/wt+3
VALUE Log ratio: log2 of PRE_VALUE

Data table
ID_REF Cy5_wt+3 Cy3_wt+3 PRE_VALUE VALUE
CM001A01 5436 5332 0.9711 -0.042308229
CM001A02 1867 2407 1.2763 0.351967481
CM001A03 4723 4803 1.0068 0.009777122
CM001A04 9963 9816 0.9754 -0.035934123
CM001A05 2228 2392 1.0629 0.088005871
CM001A06 575 1076 1.8526 0.889551419
CM001A07 6 82 13.53 3.758089934
CM001A08 2305 1948 0.8367 -0.25721766
CM001A09 2393 2564 1.0607 0.085016673
CM001A10 4380 4233 0.9568 -0.063710705
CM001A11 861 1310 1.5063 0.591009131
CM001A12 688 832 1.1972 0.259664184
CM001B01 1363 1600 1.1621 0.21673422
CM001B02 703 1292 1.8195 0.863542051
CM001B03 2676 2888 1.0684 0.095451881
CM001B04 3396 3006 0.8763 -0.190503236
CM001B05 4900 4715 0.9526 -0.070057546
CM001B06 721 880 1.2083 0.272978695
CM001B07 18322 16288 0.8801 -0.184260638
CM001B08 2293 3034 1.3099 0.389456678

Total number of rows: 11706

Table truncated, full table size 435 Kbytes.




Supplementary data files not provided

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