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Sample GSM342090 Query DataSets for GSM342090
Status Public on Nov 20, 2008
Title Non-additive expression between synthetic allopolyploid Allo738 and their progenitors
Sample type RNA
 
Channel 1
Source name Leaves before bolting
Organisms Arabidopsis thaliana; Arabidopsis arenosa
Characteristics A synthetic allopolyploid line generated by hybridization of Arabidopsis thaliana and Arabidopsis arenosa.
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using Trizol reagent (Invitrogen, San Diego) according to the manufacturer's recommendations. Each RNA sample was quantified by measuring 260/280 ratios using a UV-spectrometer (GeneQuant pro; Amersham Biosciences, Arlington Heights, IL) and by agarose–formaldehyde gel electrophoresis. Total RNA was subjected to mRNA isolation, using a Micro-FastTrack 2.0 mRNA isolation kit (Invitrogen). Equal amounts of mRNA from A. thaliana and A. arenosa were mixed as a midparent value to detect nonadditive gene expression in the allotetraploids
Label Either Cy3 or Cy5, dye-swap experiments
Label protocol We used 500 ng of mRNA in each labeling reaction using Cy3- or Cy5-dCTP (Amersham Biosciences). The Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization
 
Channel 2
Source name Artificial mix of mRNAs from Leaf tissues of A. thaliana and A. arenosa
Organisms Arabidopsis thaliana; Arabidopsis arenosa
Characteristics Arabidopsis thaliana and Arabidopsis arenosa are progenitor species of the synthetic allopolyploid line, Allo738
Extracted molecule polyA RNA
Extraction protocol Total RNA was isolated using Trizol reagent (Invitrogen, San Diego) according to the manufacturer's recommendations. Each RNA sample was quantified by measuring 260/280 ratios using a UV-spectrometer (GeneQuant pro; Amersham Biosciences, Arlington Heights, IL) and by agarose–formaldehyde gel electrophoresis. Total RNA was subjected to mRNA isolation, using a Micro-FastTrack 2.0 mRNA isolation kit (Invitrogen). Equal amounts of mRNA from A. thaliana and A. arenosa were mixed as a midparent value to detect nonadditive gene expression in the allotetraploids
Label Either Cy3 or Cy5, dye-swap experiments
Label protocol We used 500 ng of mRNA in each labeling reaction using Cy3- or Cy5-dCTP (Amersham Biosciences). The Cy3-dCTP reaction was mixed with the Cy5-dCTP reaction for one hybridization
 
 
Hybridization protocol Each lyophilized probe was re-suspended in 40 μL of
hybridization solution (0.25 M Na2HPO4, 0.25 M NaH2PO4,
pH 7.4, and 3.5% SDS, w/v). The solution was heated
for 2 min at 95 °C, chilled immediately in ice, and applied
directly to the array. After covering the array with a
24 × 40 mm coverslip (Sigma, St Louis, MO), the slide was
placed in a microarray hybridization chamber (Corning
Incorporated, Corning, NY). Hybridization was performed
overnight (16 h) at 60 °C in a hybridization oven. After
hybridization, the slides were washed for 2 min in 2× SSC,
0.03% (w/v) SDS, 2 min in 0.2× SSC, and 2 min in 0.05× SSC.
Immediately after the last wash, the slides were dried by
centrifugation (3 min at 500 r.p.m.).
Scan protocol Slides were scanned using Genepix 4000B
Description Total 8 replications ( 4 biological replications and dye-swap experiments were performed for each biological replication).
Data processing The data were processed using a lowess function to remove nonlinear components and analyzed using a linear model. This linear model was employed to partition variation in the observed data relative to technical and biological variation. Given that each feature is represented once on an array, the linear model is
Yijklm ¼ m1Ai 1Dj 1Tk 1Gl 1AGil 1DGjl 1TGkl 1TDGjkl 1eijklm
where µ represents the overall mean effect; A, D, T, and G represent main fixed effects from the array, dye, treatment (e.g., RNA from two species), and gene, respectively; and i = 1, ..., 8, k = 1, 2, j = 1, 2, and l = 1, ..., 27,648 (including 26,090 70-mer Arabidopsis oligos plus controls). The interaction terms AG, DG, TG, and TDG represent array-by-gene, dye-by-gene, treatment-by-gene, and treatment-by-dye-by-gene interactions, and {varepsilon}ijklm denotes the random error and is used to test for significance of main and interaction effects in the model. Due to confounding and/or aliasing issues involving the array, dye, and treatment terms, not all two-way interactions are included in the model. The model residuals are assumed to be normally distributed with a common variance [i.e., {varepsilon}ijklm iid N(0, {sigma}2)], unless evidence of variance nonconstancy is observed. In such a case, a per gene variance is assumed [i.e., {varepsilon}ijklm independent N(0, {sigma}l2)].
We tested differential expression using significant differences in T + TG terms for a particular gene because we are interested in changes in expression beyond the average treatment effect. The hypotheses reflect whether a gene, g, has undergone differential expression between treatments, t and t' (e.g., A. thaliana and A. arenosa).
A standard t-test statistic is used for this comparison, based on the normality assumption for the residuals. To control for multiple testing errors the false discovery rate (FDR) of BENJAMINI and HOCHBERG (1995) was employed as it provides weak control of the familywise error rate (FWER) and controls the FDR below level {alpha}. The FDR is defined as the expected proportion of incorrect rejections of H0, relative to the total number of rejections. The significance level {alpha} = 0.05 was chosen for these investigations. All analyses of variance models were fit using standard statistical packages
 
Submission date Nov 13, 2008
Last update date Nov 17, 2008
Contact name Misook Ha
E-mail(s) misook.ha@gmail.com
Phone 7732795900
Organization name National Heart Lung Blood Institute
Lab Laboratory of Epigenome Biology
Street address NIH
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL7633
Series (1)
GSE9513 Duplicate genes increase expression diversity in closely related species and allopolyploids

Data table header descriptions
ID_REF
FC Fold change of expression level, (Arabidopsis thaliana)/(Arabidopsis arenosa)
VALUE Log e ( Fold_change)
P-value Significance of expression difference
LogAllo738 Log e (average intensity of Allo738)
LogMix Log e (average intensity of equal mixture of progenitors)

Data table
ID_REF FC VALUE P-value LogAllo738 LogMix
A000001_01 0.86007 -0.15074 0.014564 8.6288 8.7795
A000010_01 1.3108 0.27061 4.0614e-05 8.9409 8.6703
A010002_01 1.1878 0.17211 0.017668 6.947 6.7749
A010003_01 1.2387 0.21409 0.00031316 7.8223 7.6082
A010009_01 0.66736 -0.40442 0.0065767 6.3624 6.7668
A010017_01 0.80467 -0.21733 0.0030397 7.4604 7.6778
A010018_01 0.94323 -0.058445 0.00078997 7.7963 7.8547
A010019_01 2.0308 0.70844 1.1545e-06 8.682 7.9736
A001002_01 0.76398 -0.26921 8.9521e-05 7.3435 7.6127
A010020_01 1.1357 0.12722 0.0090583 7.3735 7.2463
A010021_01 1.8116 0.59423 9.187e-08 9.4948 8.9005
A010024_01 1.4669 0.38313 0.00011677 7.7163 7.3332
A010027_01 1.29 0.2546 0.0054569 7.7561 7.5015
A010031_01 0.78361 -0.24384 0.0017797 6.9655 7.2094
A010033_01 0.70333 -0.35193 2.5433e-05 9.5531 9.905
A010037_01 0.30551 -1.1858 1.9394e-06 7.2773 8.463
A010039_01 1.117 0.11061 0.0019107 7.1586 7.048
A010042_01 1.307 0.2677 0.00021416 8.8896 8.6218
A010043_01 0.66292 -0.4111 1.6695e-05 7.6406 8.0517
A010050_01 0.62544 -0.4693 1.7592e-06 7.2072 7.6765

Total number of rows: 9875

Table truncated, full table size 491 Kbytes.




Supplementary file Size Download File type/resource
GSM342090__9_18_738_Cy3__Mix_Cy5_.gpr.gz 2.7 Mb (ftp)(http) GPR
GSM342090__9_19_738_Cy5__Mix_Cy3_.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM342090__9_20_738_Cy3__Mix_Cy5_.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM342090__9_21_738_Cy5__Mix_Cy3_.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM342090__9_29_738_Cy3__Mix_Cy5_.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM342090__9_30_738_Cy5__Mix_Cy3_.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM342090__9_31_738_Cy3__Mix_Cy5_.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM342090__9_32_738_Cy5__Mix_Cy3_.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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