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Sample GSM85740 Query DataSets for GSM85740
Status Public on Jun 19, 2008
Title S13_L
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: P6 F1 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: P6 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 Jun 19, 2007
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)
GSE4473 Heterosis(II, Low scan)
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 0.004753 1689.4683 24.5582 1629.5 0 1138.326 160.1416 1079 37.5 1.325295 1.330048
2 -0.4167135 747.341 30.4745 738 0 525.8981 168.9042 402 57 0.5888871 0.1721736
3 -0.413484 2146.9611 28.4024 2057 0 1070.1838 173.0962 948.5 87 1.556067 1.142583
4 0.008839 26.2045 27.4455 0 0 190.6206 184.7544 100 82 -4.377538 -4.368699
5 -0.578324 3805.2656 35.6883 3783 0 1403.187 185.9185 1377 76 2.148921 1.570597
6 -0.029564 1758.9583 28.202 1602 0 1263 219.8255 1093 96 1.312137 1.282573
7 -0.2585308 1134.9062 26.2563 1100.5 0 805.1136 204.6759 687 78 0.992871 0.7343402
8 -0.0988471 934.6328 33.97 843 0 680.3295 197.2925 601.5 50 0.7303885 0.6315414
9 -0.5268508 1225.7218 32.898 1174 0 606.8064 175.3947 568 68.5 1.060403 0.5335522
10 0.3795591 526.0367 29.4672 476.5 0 620.3944 165.2468 530 36 0.1514434 0.5310025
11 -0.305396 2413.9936 28.3478 2266.5 0 1221.4963 208.317 1146 111 1.642138 1.336742
12 -0.3738269 1165.7591 41.5698 1078 0 655.2752 212.6246 633 98 0.9755375 0.6017106
13 -0.532165 2639.1999 35.0962 2695 0 1123.9658 168.7745 1043 68 1.812238 1.280073
14 -1.196016 123.6612 35.2572 38.5 0 234.1532 206.3429 140.5 97.5 -1.517085 -2.713101
15 0.245462 1263.929 27.1613 1159 0 1162.5546 161.9905 1045.5 51.5 1.01139 1.256852
16 -1.023655 13503.9814 33.7797 16352.5 0 5763.1035 165.6163 5888 68 3.852202 2.828547
17 -0.215774 2336.1401 19.0527 2343 0 1193.4776 177 1211.5 50 1.67152 1.455746
18 1.4468205 113.8628 31.8345 29.5 0 325.5967 179.437 273 65 -2.188718 -0.7418975
19 -0.17930189 559.1193 26.3634 397.5 0 397.8165 195.5485 307 63 -0.01120421 -0.1905061
20 0.058437 1619.4776 31.2445 1537 0 1261.5872 207.1091 1163 119 1.270449 1.328886

Total number of rows: 19200

Table truncated, full table size 1558 Kbytes.




Supplementary data files not provided

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