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Series GSE3017 Query DataSets for GSE3017
Status Public on Jul 21, 2006
Title Global gene expression profiling of developing maize anthers
Organism Zea mays
Experiment type Expression profiling by array
Summary The maize spikelet contains two florets, each of which contains three anthers. Morphologically, the anthers in the upper and lower florets proceed through the same developmental program. To test for global differences in gene expression between these anthers and to identify genes that are coordinately regulated during development, RNA isolated from upper and lower floret anthers at six developmental stages was used to hybridize cDNA microarrays. Approximately 9% of the tested genes exhibited statistically significant differences in gene expression between anthers in the upper and lower florets. This suggests that several basic biological processes are differentially regulated between upper and lower floret anthers, including photosynthesis, translation, and metabolism. To identify genes that are coordinately regulated during anther development, cluster analyses were performed. A variety of patterns of gene expression were observed. Five genes involved in programmed cell death were up-regulated at the time the tapetum begins to degenerate (i.e., the early microspore stage). This finding strongly supports the hypothesis that tapetal degeneration occurs via programmed cell death. In addition, many genes involved in protein synthesis exhibited differential expression patterns during anther development. Each microarray slide was scanned multiple times. This approach led to the identification an additional 30 to 40% of statistically significant differences in gene expression as compared to a single-scan strategy.
Keywords: time course
 
Overall design Experimental aims: 1) To develop a cDNA microarray scanning approach that utilizes multiple scans of different intensities, thus maximizing the power to detecting statistically significant differences in gene expression; 2) To apply the multiple scan approach to identify differentially expressed genes in: a) the upper floret of (N)Ky21 at the selected stages of anther development; b) the lower floret of (N)Ky21 at the selected stages of anther development; and c) the upper vs. lower floret at each selected stage of anther development.
 
Contributor(s) Schnable PS
Citation(s) 16731695
Submission date Jul 27, 2005
Last update date Mar 16, 2012
Contact name Patrick S. Schnable
E-mail(s) [email protected]
Phone 515-294-0975
Organization name Iowa State University
Street address 2035B Roy J Carver Co-Lab
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platforms (1)
GPL3021 ISU Maize 12k cDNA Generation II Version B-IG
Samples (144)
GSM66053 slide1_L
GSM67527 slide1_M
GSM67528 slide1_H
Relations
BioProject PRJNA93201

Supplemental Table 1. p-values for all 398 statistically significant genes header descriptions
ID
GenBank Acc#
Statistically significant scan intensities
Low scan p-value
Medium scan p-value
High scan p-value

Data table
ID GenBank Acc# Statistically significant scan intensities Low scan p-value Medium scan p-value High scan p-value
8 AI782984 Low-Medium 0.000649564 0.000583465 0.082435839
36 DV490954 Low-Medium 0.000680467 0.000957253 0.001055255
155 DV492887 Low-Med-High 0.000363754 0.000841354 0.000448857
282 BG841334 Low 0.000943774 0.001766847 0.001501898
296 BG840735 High-Medium 0.013178561 0.000112292 5.00281E-05
326 BM336429 Low-Medium 0.00076266 0.000582551 0.002137643
340 BG840178 Low-Med-High 0.000270147 0.000548559 0.000178613
342 BM073171 Low 0.000336869 0.003100968 0.001700741
344 BQ538817 Low-Med-High 0.000104207 0.000136606 6.83801E-05
417 AW042168 Low-Med-High 0.000154374 0.000163701 0.000135128
423 DV489574 Low-Medium 0.000736314 0.000196042 0.004002897
467 AW400366 High-Medium 0.001009668 0.000797905 0.000505798
478 AW424649 Low-Med-High 0.000190831 0.000347494 0.000342683
494 DV550704 High-Medium 0.001546574 0.000755179 0.000329801
510 AI734304 Low 0.000672204 0.001251983 0.089400871
516 DV492043 High 0.003010903 0.002047799 0.000913894
536 AI770330 High-Low 0.000586522 0.001082144 0.000557818
538 DV493039 High 0.001384892 0.001551406 0.00081479
613 AI491628 High-Medium 0.001097146 0.00036727 0.000601696
762 DV491115 High 0.00178101 0.001232766 0.000866155

Total number of rows: 398

Table truncated, full table size 23 Kbytes.




Supplemental Table 2. Summary of fold-change validation data for the stage comparisons header descriptions
ID
GenBank Acc#
Comparison
p-stage scan(s)
Stage comparison in QRT-PCR
Microarray Fold Change
QRT-PCR Fold Change for Biological Replicate 1 The fold change for each biological replicate was calculated from three technical replicates.
QRT-PCR Fold Change for Biological Replicate 2 The fold change for each biological replicate was calculated from three technical replicates.

Data table
ID GenBank Acc# Comparison p-stage scan(s) Stage comparison in QRT-PCR Microarray Fold Change QRT-PCR Fold Change for Biological Replicate 1 QRT-PCR Fold Change for Biological Replicate 2
494 DV550704 Stage Medium-High 1 vs. 6 2.69 3.90 28.07
768 AI783020 Stage Medium-High 5 vs. 4 0.24 5.79 5.10
1617 DV549778 Stage Low 5 vs. 4 0.17 0.18 0.24
1634 DV550234 Stage Low 1 vs. 6 0.43 0.38 0.98
1637 DV549710 Stage Low 5 vs. 4 0.49 0.99 0.76
1926 DV491034 Stage Low 1 vs. 6 4.35 4.93 9.66
1968 DV549714 Stage Low 1 vs. 6 2.17 1.38 5.44
2031 AI737193 Stage Low-Medium 5 vs. 4 0.40 0.33 0.24
3942 DV495048 Stage High 5 vs. 4 0.33 0.27 0.32
4929 DV942660 Stage Low 5 vs. 6 4.68 2.04 7.09
5337 AI861540 Stage Medium-High 5 vs. 4 1.58 1.14 0.95
5444 DV492481 Stage Medium-High 5 vs. 4 0.40 0.30 0.30
7278 DV490367 Stage Medium-High 5 vs. 4 0.49 0.38 0.60
8066 DV549910 Stage Medium-High 5 vs. 4 3.21 1.53 1.61
8911 DV489988 Stage Medium-High 5 vs. 4 8.33 270.64 100.68
9352 AW256092 Stage High 5 vs. 4 0.28 0.37 0.99
11783 DV489907 Stage High 5 vs. 4 0.69 0.58 0.75

Total number of rows: 17


Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE3017_supplementaryFig1.pdf 28.2 Kb (ftp)(http) PDF
GSE3017_supplementaryFig2.pdf 19.2 Kb (ftp)(http) PDF

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