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Sample GSM78597 Query DataSets for GSM78597
Status Public on Oct 22, 2005
Title B46/o2 dye-swap rep1 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 1072.375 972.5186246 264.0909091 228.7449857
2 528.7613636 747.8198198 283.4827586 299.3201133
3 3174.103448 1336.427966 1022.022472 222.7692308
4 2949.47561 1336.655914 935.1494253 251.350365
5 796.9310345 1288.048507 197.2840909 184.6691176
6 752.1744186 1252.851613 191.0454545 177.340836
7 1063.590909 1216.992647 190.9886364 308.8937729
8 1152.625 1116.155963 206.0795455 320.5183486
9 2078.046512 1056.309524 761.3707865 188.6391753
10 2665.916667 1044.779221 865.8131868 203.2857143
11 925.5581395 1167.614731 168.6704545 181.305949
12 826.7931034 1043.507463 232.9318182 197.6915423
13 934.4318182 1164.651064 184.3522727 165.8589744
14 1003.329545 1328.388112 255.1136364 212.3041958
15 4838.88172 1979.368421 1789.431373 297.710084
16 4835.877778 1754.217593 1890.20202 271.3381643
17 978.75 1584.106599 189.4204545 216.3756345
18 1195.113636 1794.955285 203.0689655 237.2579365
19 2438.351064 1955.324444 611.2736842 356.2355556
20 2272.102273 1620.737952 539.1704545 328.7319277

Total number of rows: 16560

Table truncated, full table size 994 Kbytes.




Supplementary data files not provided

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