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Sample GSM85737 Query DataSets for GSM85737
Status Public on Dec 06, 2005
Title S12_M
Sample type RNA
 
Channel 1
Source name Seedling stage above ground tissue
Organism Zea mays
Characteristics Genotype: B73
Tissue: above ground seedling
Dev stage: 14 days old
Sample name: P5 B73 Cy3
Extracted molecule total RNA
Extraction protocol total RNA extraction with Trizol (Invitrogen, Carlsbad, CA) with minor modifications to manufacturer’s instructions, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer’s instructions
Label Cy3
Label protocol Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dy molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.
 
Channel 2
Source name Seedling stage above ground tissue
Organism Zea mays
Characteristics Genotype: Mo17
Tissue: above ground seedling
Dev stage: 14 days old
Sample name: P5 Mo17 Cy5
Extracted molecule total RNA
Extraction protocol total RNA extraction with Trizol (Invitrogen, Carlsbad, CA) with minor modifications to manufacturer’s instructions, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer’s instructions
Label Cy5
Label protocol Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/. Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dy molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.
 
 
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 -0.103561 5004.5986 136.0716 4768 21 3926.3291 259.1932 3581.5 152 1.218701 1.11514
2 -0.36810481 2100.4025 146.4498 2078 19 1535.937 227.7974 1438 117 0.4566841 0.08857929
3 0.22336 3806.0932 94.1597 3936 0 4234.4565 210.2282 4033 76 1.033105 1.256465
4 -0.967872 228.2528 100.4288 148 0 289.0574 214.1745 201 108 -1.878493 -2.846365
5 0.122493 7683.7905 135.2779 7826 5 6370.3559 213.8354 6718 66 1.686463 1.808956
6 0.213787 5926.2915 110.7517 5711 0 5766.6567 218.7046 5549 100 1.383905 1.597692
7 0.1570893 3920.2968 127.5149 3777 0 3630.6127 210.8934 3690 97.5 0.9973217 1.154411
8 0.6803128 2424.7534 100.3951 2303.5 0 3728.1716 183.5813 3891 62.5 0.5203482 1.200661
9 -0.267275 3101.6364 95.6515 3086.5 0 2340.5437 226.8583 2181.5 137 0.8268453 0.5595703
10 0.49342574 807.4666 108.1306 754 0 1376.9066 160.1368 1287 60.5 -0.513036 -0.01961026
11 -0.33593 8368.4091 126.6276 8639 0 4857.4057 176.4246 4772.5 72 1.791813 1.455883
12 -0.0041326 2732.7807 107.6615 2838 0 2740.2465 205.5541 2519.5 91.5 0.7392379 0.7351053
13 0.139448 4786.3369 118.2171 4833.5 0 4493.4047 230.1119 4477.5 107 1.227424 1.366872
14 0.0072839 492.7172 105.6932 468 0 600.559 186.1769 561 82.5 -0.978018 -0.9707341
15 -0.17971485 1707.7852 107.1825 1497 0 1427.8636 185.9278 1283 83.5 0.1549978 -0.02471705
16 0.151863 32236.7656 141.9384 36680.5 0 30236.2734 278.9716 32529.5 138 3.235874 3.387737
17 -0.346127 9093.9824 102.6123 9370 0 5149.1743 176.323 5087 75 1.869597 1.52347
18 0.1973 386.3379 111.3107 282 0 539.4345 198.4073 457 92 -1.460659 -1.263359
19 -0.325801 2791.4675 121.016 2212 0 1731 177.9162 1515.5 56.5 0.5209991 0.1951981
20 -0.394171 7116.4892 131.7871 7453 0 4172.1459 233.0063 4025 141 1.651728 1.257557

Total number of rows: 19200

Table truncated, full table size 1620 Kbytes.




Supplementary data files not provided

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