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Sample GSM78977 Query DataSets for GSM78977
Status Public on Oct 22, 2005
Title M14/o2 dye-swap rep1 array1
Sample type RNA
 
Channel 1
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 Cy5
Label protocol http://www.maizegdb.org/documentation/mgdp/microarray/protocols.php
 
Channel 2
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 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 CH1 and CH2 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 (CH1/CH2) 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 1428.712766 1631.814332 748.0736842 1043.129032
2 1237.589474 1385.22541 766.5684211 1017.220408
3 1576.414894 1237.062937 1895.697248 487.4666667
4 1771.670213 1203.667832 1745.01 524.3799283
5 1081.043011 1050.030973 497.9468085 432.3938053
6 943.0340909 1101.314448 418.6781609 440.2067989
7 914.0752688 988.50625 406.1612903 385.96875
8 836.287234 922.1315789 329.0957447 360.7744361
9 1125.042553 1007.252632 972.5670103 389.2616487
10 1072.287234 1038.335664 784.6989247 393.0629371
11 933 1005.606195 320.5625 355.5242291
12 1016 933.3024194 454.4680851 336.4475806
13 952.8617021 1003.744361 362.4787234 376.7811321
14 1009.234043 993.2754098 356.1290323 349.9147541
15 2792.839286 1084.68 3417.33913 329.0559006
16 3064.104348 1104.849231 3831.675 363.48125
17 969.7446809 1130.915842 346.6489362 654.8382353
18 937.9684211 1119.220339 391.1473684 380.3121387
19 1327.829787 1275.863636 1340.855422 403.9023569
20 1379.978723 1316.915493 1206.045977 403.2852234

Total number of rows: 16560

Table truncated, full table size 993 Kbytes.




Supplementary data files not provided

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