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Sample GSM85684 Query DataSets for GSM85684
Status Public on Dec 06, 2005
Title S1_M
Sample type RNA
 
Channel 1
Source name Seedling stage above ground tissue
Organism Zea mays
Characteristics Genotype: F1
Tissue: above ground seedling
Dev stage: 14 days old
Sample name: P2 F1 Cy3
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Seedling stage above ground tissue
Organism Zea mays
Characteristics Genotype: B73
Tissue: above ground seedling
Dev stage: 14 days old
Sample name: P2 B73 Cy5
Extracted molecule total RNA
Label Cy5
 
 
Hybridization protocol Fluorescent targets were hybridized as described in the “cDNA microarray protocol” file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.
Scan protocol Each microarray chip (27 total) was scanned a minimum of six times in ascending amounts of laser power and PMT gain settings. Slides 1-15 were scanned using the ScanArray5000 (Packard, Meriden, CA). Slides 16-27 were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA). Two scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.
Description Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage. Total RNA was isolated from nine replications of B73, Mo17, and F1 maize seedling genotypes (6 individual seedlings pooled for each genotype in each replication) using Trizol reagent (Invitrogen, Carlbad, CA) with slight modifications to manufacturer’s protocol. Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer’s protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications. Each sample was labeled with Cy dye and hybridize to the GP2613 platform.
Data processing The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide. Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications. Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides. Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).
 
Submission date Dec 01, 2005
Last update date Dec 05, 2005
Contact name Patrick S. Schnable
E-mail(s) schnable@iastate.edu
Phone 515-294-0975
Organization name Iowa State University
Street address 2035B Roy J Carver Co-Lab
City Ames
State/province IA
ZIP/Postal code 50011
Country USA
 
Platform ID GPL2613
Series (2)
GSE3733 Modes of gene action observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents
GSE4477 Heterosis

Data table header descriptions
ID_REF
VALUE Normalized log ratio value of background corrected intensities of red channel and green channel
Ch1_Signal Mean Pixel intensity avaeraged over the local signal region for green channel (Cy3)
Ch1_Background Mean Pixel intensity avaeraged over the local background region for green channel (Cy3)
Ch1_Signal Median Median pixel intensity computed over the local signal region for green channel (Cy3)
Ch1_Background Median Median pixel intensity computed over the local background region for green channel (Cy3)
CH2_Signal Mean Pixel intensity avaeraged over the local signal region for red channel (Cy5)
Ch2_Background Mean Pixel intensity avaeraged over the local background region for red channel (Cy5)
Ch2_Signal Median Median pixel intensity computed over the local signal region for red channel (Cy5)
Ch2_Background Median Median pixel intensity computed over the local background region for red channel (Cy5)
Ch1_norm Background corrected and normalized log value of green channel(Cy3)
Ch2_norm Background corrected and normalized log value of red channel(Cy5)

Data table
ID_REF VALUE Ch1_Signal Mean Ch1_Background Mean Ch1_Signal Median Ch1_Background Median CH2_Signal Mean Ch2_Background Mean Ch2_Signal Median Ch2_Background Median Ch1_norm Ch2_norm
1 -0.3673 6487.5629 104.7228 6498 0 3472.8132 255.6967 3371 105 1.461579 1.094279
2 0.1420511 3382.9472 144.2196 3363 0 3006.1679 240.9507 2946 93 0.8100692 0.9521203
3 -0.767618 8605.4931 95.855 9004.5 0 3476.831 260.7524 3155 129 1.786681 1.019063
4 2.055927 105.0666 94.7989 0 0 246.2045 230.3387 137.5 98 -6.334899 -4.278972
5 -0.218395 9370.705 103.462 9625.5 0 5876.5781 283.146 5736 163 1.850682 1.632287
6 0.2120045 3517.6782 78.7028 3550 0 3931.8759 297.2097 3416 198 0.8623165 1.074321
7 0.1120853 2506.1782 104.2705 2565 0 2289.6748 283.2663 2318 177 0.5461701 0.6582554
8 0.4747841 2231.496 97.9946 2080 0 2730.0761 232.8762 2633 134 0.3373462 0.8121303
9 -0.3158175 2729.8793 103.8641 2655 0 1764.8201 255.2101 1560 95 0.5877568 0.2719393
10 0.7107527 1634.3687 111.3211 1439 0 2554.0222 248.374 2350 110 -0.0194251 0.6913276
11 0.182364 5733.4711 106.2951 5636 0 5234.0913 283.8272 5061 163 1.318178 1.500542
12 -0.919647 10239.4472 118.3299 10957 0 3698.5461 249.4949 3281 121 1.982471 1.062824
13 -0.023919 6080.5312 142.5016 6255 0 4588.9619 331.4918 4599.5 177 1.422364 1.398445
14 0.7767543 637.768 86.6171 519 0 1114.7741 284.7548 1047.5 127 -1.006048 -0.2292937
15 -0.0813149 3539.1118 90.9015 3485.5 0 2563.2954 266.068 2501.5 127 0.8478792 0.7665643
16 0.294811 32607.6757 159.3365 38200 0 33743.8671 331.2 36652 218 3.221959 3.51677
17 -0.17812 8507.0556 109.2816 8358 0 5457.6416 293.3015 5251 197 1.711087 1.532967
18 1.18109485 471.2177 135.7485 399.5 0 1514.1015 299.967 1238.5 185 -1.271366 -0.09027115
19 0.47565521 1250.7294 103.1887 946 0 1473.9583 295.9298 1397.5 162 -0.4087447 0.06691051
20 -0.3492549 4538.6513 81.7069 4662.5 0 2665.1437 253.747 2540 128.5 1.135011 0.7857561

Total number of rows: 19200

Table truncated, full table size 1633 Kbytes.




Supplementary data files not provided

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