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Sample GSM78984 Query DataSets for GSM78984
Status Public on Oct 22, 2005
Title M14/o2 dye-swap rep3 array2
Sample type RNA
 
Channel 1
Source name M14 o2 endosperm 14 DAP
Organism Zea mays
Characteristics Line: M14 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 M14 wild type endosperm 14 DAP
Organism Zea mays
Characteristics Line: M14 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 20, 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
1 673.09375 554.4469697 622.3854167 550.9015152
2 620.4631579 546.5676692 583.5957447 466.9473684
3 1520.113402 235.2857143 1051.835052 240.8204082
4 1913.693182 187.8968254 1156.454545 241.2539683
5 554.125 160.2773973 357.2386364 197.2636986
6 484.8636364 149.4880952 365.2159091 194.1349206
7 189.4545455 135.4554795 210.9772727 184.1678082
8 206.2386364 134.297619 315.5795455 164.1706349
9 317.1363636 228.9931507 338.0909091 340.9863014
10 402.1022727 153.1349206 398.3863636 265.5634921
11 223.3522727 180.3479853 342.8863636 218.1062271
12 306.4431818 175.4908425 406.7011494 202.03663
13 266.9545455 180.0297872 303.2045455 158.5446809
14 230.3636364 144.2182741 252.2727273 174.0609137
15 895.6477273 145.8047945 806.25 168.4935065
16 1027.858974 144.3178808 622.6363636 174.489726
17 207.7840909 159.5944882 254.5454545 199.980315
18 228.9545455 138.6456693 275.7613636 167.3503937
19 291.8888889 154.9323843 295.3222222 630.4448276
20 317.0909091 142.8116438 296.1363636 219.3150685

Total number of rows: 16560

Table truncated, full table size 997 Kbytes.




Supplementary data files not provided

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