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Sample GSM406013 Query DataSets for GSM406013
Status Public on Nov 20, 2009
Title 13463244
Sample type RNA
 
Channel 1
Source name Seedling stage above ground tissue
Organism Zea mays
Characteristics genotype: MxRILM0030
tissue: Above ground seedling
developmental stage: 14 days old
sample name: Rep 3 MxRILM0030
Extracted molecule total RNA
Extraction protocol total RNA extraction with Trizol, 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/
 
Channel 2
Source name Seedling stage above ground tissue
Organism Zea mays
Characteristics genotype: RILM0030
tissue: Above ground seedling
developmental stage: 14 days old
sample name: Rep 3 RILM0030
Extracted molecule total RNA
Extraction protocol total RNA extraction with Trizol, 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 dye 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 was scanned a minimum of four times with constant PMT and increasing laser power settings. Slides were scanned with a Pro Scan Array HT (Perkin Elmer, Wellesley, MA).
Description Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage. Total RNA was isolated from four replications of RIL@, B73xRIL, and Mo17xRIL for 30 RILs (with 6 individual seedlings pooled for each genotype in each replication) using Trizol reagent. 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 hybridized to the GPL3333 platform (4 replications) and GPL3538 platform (2 replications).
Data processing All scans from each slide were quantified using ImaGene (BioDiscovery, El Segundo, CA). For each slide and dye combination, median scan intensities were extrapolated using data from the multiple scans collected using a variation of a previously published linear regression method (DUDLEY et al. 2002). Non-informative spots were removed prior to analysis. In total, 14,401 (GPL3333) and 14,260 (GPL3538) informative spots were analyzed. Within-slide correlation coefficient between the Cy3 and Cy5 background-corrected raw signal intensities was used to quantify the quality of each slide in the eQTL experiment. A correlation coefficient cutoff of 0.90 flagged 4% (N=15) of the SAM1.1 slides for removal prior to analysis. In many cases, these slides had visually apparent technical artifacts. Using the same cutoff for SAM3.0 slides, less than 1% (N=1) of the slides were below this cutoff, and none were removed. For the remaining slides, lowess normalization was applied to the natural log (ie, log base e) of the background-corrected raw signal intensities to remove signal-intensity-dependent dye effects on each slide (CUI et al. 2003; DUDOIT et al. 2002). Normalization was conducted separately for each slide to avoid introducing dependencies among expression values. After normalization, data for each slide/dye combination were median-centered so expression measures would be comparable across slides. Post-normalized data was summarized by taking the average of all technical and biological replicates within a genotype.
 
Submission date May 20, 2009
Last update date Nov 20, 2009
Contact name Patrick S. Schnable
E-mail(s) [email protected]
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 GPL3538
Series (1)
GSE16136 Regulation of Gene Expression and Parent-of-Origin Effects in Maize Hybrids

Data table header descriptions
ID_REF
VALUE Normalized log e ratio value of background corrected intensities of red channel and green channel (ch2_norm - ch1_norm)
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 0.059878 1513.0079 270.0859 1408.0 188.5 1037.6879 174.3377 1012.0 140.0 0.073608226418889 0.133485747296603
2 -0.188327 1715.0328 272.7651 1656.5 209.0 943.2649 172.4795 898.0 147.0 0.202407015041025 0.0140800293686549
3 -0.028911 881.3563 228.9747 629.0 163.0 557.6558 158.1282 465.0 131.0 -0.559343798295176 -0.588254663762183
4 -0.110669 943.4926 223.3405 901.0 171.0 561.9091 171.4848 491.0 138.0 -0.485781094093828 -0.596450235093823
5 -0.379393 856.3656 247.6989 747.5 192.5 429.3006 192.7617 357.0 157.0 -0.64754868236623 -1.02694120597941
6 -0.172178 758.3181 251.4885 677.5 194.5 434.3656 177.6742 396.0 151.0 -0.813018705471311 -0.985196637876454
7 0.295725 301.9181 221.5209 246.0 161.0 238.2906 177.3922 206.5 140.0 -2.26704464139034 -1.97131945110394
8 0.053748 4181.2001 267.6827 4049.0 201.0 2920.0114 191.3292 2927.0 154.0 1.18940750847322 1.24315596130699
9 -0.125924 1939.0208 267.4723 1827.5 193.0 1124.7581 161.0311 1067.0 137.0 0.35250931001663 0.226584864858264
10 -0.427024 11119.2177 290.9875 12503.5 183.5 4895.725 186.6419 5628.0 134.5 2.20650917130507 1.77948540113849
11 -0.349510 4776.8237 269.3966 5028.0 203.0 2292.1701 214.2479 2399.0 173.0 1.32729065161254 0.977780257629216
12 0.605567 527.688 226.1148 477.0 160.0 579.1864 199.7701 552.5 177.5 -1.24163792670108 -0.636070879517996
13 0.562312 221.1822 219.3852 167.0 172.0 194.1865 178.9944 168.0 154.0 -3.35948059726310 -2.79716816361147
14 -0.018619 862.2014 224.4016 779.5 162.0 563.5839 168.2438 530.0 144.0 -0.585430914945137 -0.60405031974989
15 0.075911 942.2963 231.5847 827.0 167.0 659.3873 164.255 591.5 142.5 -0.477979547256989 -0.402068891058394
16 -0.131243 1035.7553 237.5447 957.0 167.0 611.0666 174.5683 565.0 141.0 -0.364399923325871 -0.49564269039935
17 0.165414 1806.2207 241.6149 1815.0 178.0 1366.1523 177.4225 1435.0 132.0 0.283444843997439 0.448859180659653
18 -0.430527 1922.0128 237.2765 1753.0 185.0 847.0365 163.6608 803.0 126.0 0.345399300837537 -0.0851276891264039
19 -0.837452 534.2129 227.6574 435.0 168.0 212.9816 154.0629 199.0 126.0 -1.28676079894021 -2.12421306735766
20 0.052275 371.1477 225.0634 330.5 166.0 241.4545 157.8616 222.0 125.0 -1.87223417000276 -1.81995955941693

Total number of rows: 16000

Table truncated, full table size 1698 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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