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Sample GSM78599 Query DataSets for GSM78599
Status Public on Oct 22, 2005
Title B46/o2 dye-swap rep2 array2
Sample type RNA
 
Channel 1
Source name B46 o2 endosperm 14 DAP
Organism Zea mays
Characteristics Line: B46 opaque2 mutant
Tissue: Endosperm
Stage: 14 DAP
Extracted molecule polyA RNA
Extraction protocol mRNA was extracted from the frozen immature endosperm tissue with the PolyATract System 1000 mRNA isolation kit (Promega, Madison, WI) according to the manufacturer's instructions.
Label Cy5
Label protocol http://www.maizegdb.org/documentation/mgdp/microarray/protocols.php
 
Channel 2
Source name B46 wild type endosperm 14 DAP
Organism Zea mays
Characteristics Line: B46 wild type
Tissue: Endosperm
Stage: 14 DAP
Extracted molecule polyA RNA
Extraction protocol mRNA was extracted from the frozen immature endosperm tissue with the PolyATract System 1000 mRNA isolation kit (Promega, Madison, WI) according to the manufacturer's instructions.
Label Cy3
Label protocol http://www.maizegdb.org/documentation/mgdp/microarray/protocols.php
 
 
Hybridization protocol http://www.maizegdb.org/documentation/mgdp/microarray/protocols.php
Scan protocol The slide was scanned using a laser scanner (ScanArray 5000, GSI Lumonics- Packard BioScience, Billerica, MA) for both channel 1 (Cy3) and 2 (Cy5) at 10 um resolution.
Description The channel 1 and channel 2 images were analyzed using ImaGene 4.1 software (BioDiscovery, Marina Del Rey, CA) to obtain average signal and background intensities for each spot.
Data processing The control and empty spots were removed first. The background of each spot was subtracted from the signal, and then the background-subtracted signal intensity of duplicate spots within each slide was averaged. LOWESS normalization was used to remove the dye bias. The log ratio of normalized CH2 and CH1 was calculated.
 
Submission date Oct 18, 2005
Last update date Oct 21, 2005
Contact name Hongwu Jia
E-mail(s) jiahongwu@yahoo.com
Organization name Iowa State University
Department Agronomy
Lab Paul Scott
Street address 1407 Agronomy Hall
City Ames
State/province IA
ZIP/Postal code 50010
Country USA
 
Platform ID GPL2984
Series (1)
GSE3490 Comparison of Transcript Profiles in Wild-type and o2 Maize Endosperm in Different Genetic Backgrounds

Data table header descriptions
ID_REF
VALUE Normalized log ratio (CH2/CH1) using LOWESS normalization
CH1_SIG_MEAN Channel 1 (cy5) signal mean
CH1_BKD_MEAN Channel 1 (cy5) background mean
CH2_SIG_MEAN Channel 2 (cy3) signal mean
CH2_BKD_MEAN Channel 2 (cy3) background mean

Data table
ID_REF VALUE CH1_SIG_MEAN CH1_BKD_MEAN CH2_SIG_MEAN CH2_BKD_MEAN
1 618.5402299 542.6133829 525.6162791 401.5092937
2 560.091954 474.6402439 581.5348837 522.1355422
3 2388.038462 541.7469512 1043.45977 378.6438356
4 2546.888889 575.2304965 1287.477273 467.8901099
5 430.862069 454.4945055 536.9885057 375.021978
6 422.9885057 802.7301587 468.9545455 303.6944444
7 735.4337349 810.079096 520.9772727 419.3569405
8 550.3522727 628.3754647 493.3181818 379.6988848
9 1426.954545 524.9449541 1000.897727 481.7588424
10 1686.779412 719.2105263 1199.056818 532.7395833
11 585.4791667 704.8679868 471.5463918 475.6666667
12 636.7727273 598.0643087 639.8863636 432.7588424
13 778.5862069 793.7588424 577.3563218 433.3376206
14 666.9886364 554.6433824 567.0344828 418.2490842
15 3656.046729 610.2720588 1672.733333 488.1206897
16 3029.42 879.0207469 1735.623529 535.5019455
17 583.0227273 997.9816514 521.7191011 568.8156682
18 498.1704545 694.1993569 536.3409091 551.266881
19 2658.77381 705.7588424 1859.693182 461.6688103
20 2176.448276 798.1865079 853.8068182 505.9007937

Total number of rows: 16560

Table truncated, full table size 998 Kbytes.




Supplementary data files not provided

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