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Sample GSM78978 Query DataSets for GSM78978
Status Public on Oct 22, 2005
Title M14/o2 dye-swap rep1 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 (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
1 513.5106383 741.3154122 253.5106383 208.2321429
2 546.5483871 705.4832536 231.4255319 216.9622642
3 1646.731183 913.4857143 655.94 149.3891213
4 1742.105769 1109.229249 806.184466 181.8976378
5 472.3297872 958.9283019 100.4042553 136.9473684
6 490.5744681 969.430605 130.5 112.9755245
7 867.6489362 1083.231441 114.1276596 161.1746725
8 799.3510638 1070.237762 151.4574468 135.5034965
9 1258.797872 1085.491803 496 157.5384615
10 1279.170213 1184.865169 390.9893617 189.8539326
11 1088.744681 1071.243816 144.5957447 102.8485915
12 593.1413043 1009.881844 137.8085106 132.5273775
13 753.0319149 1247.825911 197.2234043 141.766129
14 834.712766 1241.31338 234.5957447 130.3556338
15 1738.755319 1420.535948 1190.491228 161.034965
16 2071.572816 1451.749004 1236.284483 164.8244898
17 1319.146067 1652.829582 660.8795181 206.9580645
18 843.5106383 1578.139098 123.212766 166.5714286
19 1623.188889 1747.629179 558.1235955 184.5333333
20 1467.329787 1760.690402 574.6202532 151.5044776

Total number of rows: 16560

Table truncated, full table size 993 Kbytes.




Supplementary data files not provided

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