NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM63370 Query DataSets for GSM63370
Status Public on Jan 01, 2006
Title cDNA array +3wt/-3wt 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 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 +3 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 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 5962 4024 1.4646 0.550506701
CM001A02 1234 1626 0.7502 -0.414652832
CM001A03 4834 4768 1.0022 0.003170443
CM001A04 7858 2235 3.4755 1.797220545
CM001A05 2746 4593 0.591 -0.758769964
CM001A06 246 701
CM001A07 7 -7
CM001A08 1991 3188 0.6173 -0.695956304
CM001A09 3452 4200 0.8125 -0.299560282
CM001A10 2256 2070 1.0773 0.107420059
CM001A11 404 1567 0.2549 -1.971996722
CM001A12 791 796
CM001B01 772 1401 0.5447 -0.876466228
CM001B02 559 10023 0.0551 -4.181803871
CM001B03 1714 2506 0.6761 -0.564691448
CM001B04 3169 3582 0.8745 -0.193469711
CM001B05 3074 3473 0.8749 -0.192809967
CM001B06 549 2084 0.2604 -1.941198646
CM001B07 16859 4901 3.4004 1.765704465
CM001B08 3241 3704 0.8649 -0.209394757

Total number of rows: 11694

Table truncated, full table size 434 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.