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Sample GSM79040 Query DataSets for GSM79040
Status Public on Oct 22, 2005
Title Mixed wild type/mixed o2 dye-swap rep1 array1
Sample type RNA
 
Channel 1
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 Cy5
Label protocol http://www.maizegdb.org/documentation/mgdp/microarray/protocols.php
 
Channel 2
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 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 1241.946237 1210.009877 244.2826087 283.9521411
2 653.3052632 687.6677316 445.5416667 471.5909091
3 1679.322917 1429.359155 585.3473684 224.9508772
4 1550.736842 1361.366038 916.1358025 204.5827338
5 976.4148936 1261.35426 163.7894737 165.1377778
6 1020.510638 1282.85782 200.6421053 181.5745614
7 1280.726316 1437.992395 180.8 184.0451128
8 1279 1408.384868 167.3191489 159.6688742
9 1277 1426.494624 412.7765957 183.4487633
10 1456.831579 1503.217391 336.1052632 176.3815029
11 1440.453608 1600.384615 190.5773196 176.4770992
12 875.6105263 1348.920168 164.8526316 169.7813765
13 1114.515789 1586.729508 242.2421053 170.4534413
14 1120.326316 1615.241636 217.6421053 203.6487455
15 2305.515789 1931.157377 2151.763441 203.3355049
16 2121.642105 1979.533333 2112.89899 229.5409253
17 1291.90625 1825.285714 183.2083333 214.2927757
18 1129.5 1925.244582 181.5684211 189.1724138
19 1608.135417 1881.590476 706.96875 208.1790123
20 1633.831579 2044.615635 849.1052632 223.7747253

Total number of rows: 16560

Table truncated, full table size 996 Kbytes.




Supplementary data files not provided

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