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Sample GSM79037 Query DataSets for GSM79037
Status Public on Oct 22, 2005
Title Mixed wild type/mixed o2 dye-swap rep1 array2
Sample type RNA
 
Channel 1
Source name Mixed 8 o2 mutant lines endosperm 14 DAP
Organism Zea mays
Characteristics Lines: A619 opaque2 mutant, B14A opaque2 mutant, B45 opaque2 mutant, B46 opaque2 mutant, B57 opaque2 mutant, B66 opaque2 mutant, B73 opaque2 mutant, and 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 Mixed 8 wild type lines endosperm 14 DAP
Organism Zea mays
Characteristics Lines: A619 wild type, B14A wild type, B45 wild type, B46 wild type, B57 wild type, B66 wild type, B73 wild type, and 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 4350.770833 5172.008824 777.3684211 874.8575581
2 3726.319588 4517.375912 760.15625 754.4487633
3 4795.181818 4812.924658 1075.056818 624.7847222
4 3688.701149 3323.393836 672.5113636 425.9760274
5 2703.556818 3105.38961 343.2068966 356.5219298
6 2789.818182 3273.295302 402.7613636 372.4313725
7 3579.397727 3479.401929 398.5287356 370.0128617
8 3752.988636 3222.919414 837.5977011 362.1684982
9 3327.863636 3157.284133 569.2272727 400.9413919
10 3328.054945 3431.440613 529.8586957 391.2226415
11 3068.642105 3287.779264 286.9791667 339.4069401
12 2463.344828 2925.488599 358.5 365.3373494
13 3127.068182 3137.06383 398.7954545 337.4851064
14 2460.931034 3104.508547 357.5795455 331.5702128
15 5390.59542 3227.104348 2685.212598 294.1974249
16 5800.513761 3166.543478 2885.178571 325.2913043
17 2017.639535 2928.192661 283.8636364 270.2925764
18 2065.643678 2672.693333 273.1494253 256.8698885
19 3107.090909 2930.459677 499.2613636 272.4112903
20 3118.170455 3113.897106 445.8977273 269.3954984

Total number of rows: 16560

Table truncated, full table size 999 Kbytes.




Supplementary data files not provided

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