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Sample GSM213692 Query DataSets for GSM213692
Status Public on Nov 20, 2008
Title Comparative genomic hybridization between Arabidopsis thaliana and Arabidopsis arenosa
Sample type genomic
Channel 1
Source name Genomic DNA from Arabidopsis thaliana autotetraploid
Organism Arabidopsis thaliana
Characteristics A. thaliana isogenic autotetraploids (At4, accession no. CS3900)
Biomaterial provider Chen Lab
Growth protocol All plants were grown in a growth chamber at 22° and under 16 hr of light per day at the University of Washington with two biological replications. Leaves were collected from 20 plants in each biological replication prior to bolting (with seven to eight rosette leaves) in each line.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated and sheared using a sonicator.
Label Cy3, Cy5 dye-swap
Label protocol DNA targets were prepared by the direct incorporation of fluorescently labelled deoxyribonucleotides (Cy3- and Cy5-dCTP) during one round of DNA synthesis. An aliquot of 1 µg of total genomic DNA was mixed with 2 µg of random nanomer primer. The mixture was incubated at 95 °C for 5 min, chilled on ice, and then added to a reaction mix (50 µL) with a final composition of 500 µm each of dATP and dGTP and 100 µm of dTTP and Cy3-dCTP or Cy5-dCTP and Klenow DNA polymerase. The reaction was incubated at 37 °C for 8 h.
Channel 2
Source name Arabidopsis arenosa leaves
Organism Arabidopsis arenosa
Characteristics A. arenosa (Aa, accession no. CS3901)
Biomaterial provider Chen Lab
Treatment protocol The same as Channel 1
Growth protocol The same as Channel 1
Extracted molecule genomic DNA
Extraction protocol The same as Channel 1
Label Cy3, Cy5 dye swap
Label protocol The same as Channel 1
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 8 replicates with dye-swap experiments
Data processing The notation Xijkplm is used to denote the mth replicate spot of gene l with feature type p under target condition k labelled with dye j on slide i. After log transformation, Yijkplm = log(Xijkplm).
The anova model for this situation is given by:
Yijkplm = µ + Si + Dj + Tk + Fp + Gl + TFkp + SGil + DGjl + TGkl + FGpl + TFGkpl + ijkplm,where µ represents the overall mean effect, S, D, T, F and G represent main effects from the slide, dye, target (e.g. A.thaliana genome vs. A.arenosa genome), feature type (e.g. oligo vs. gene) and gene, respectively. The interaction terms TF, SG, DG, TG, FG and TFG represent target by feature type, array by gene, dye by gene, target by gene, feature type by gene, and target by feature type by gene interactions, and ijkplm 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 slide, dye and target 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. ijkplm i.i.d. N(0, σ2)). Also, a per gene variance is assumed (i.e. ijkplm independent.
Hypothesis testing
The presence of differential expression in a microarray expression is represented by significant differences in T + TG terms for a particular gene. The following hypotheses are tested to determine whether a gene, g, has undergone differential expression between targets t and t' (e.g. A.thaliana RNA vs. A. arenosa RNA).
H0: Tt + TGtg = Tt' + TGt'g
A standard t-test statistic is used for this comparison, based on the normality assumption for the residuals. To control for multiple testing errors, both Holm's and the false discovery rate (FDR) were employed. Holm's sequential adjustment provides strong control of the family-wise error rate (FWER) below level α with greater power than the standard Bonferroni method (Hochberg and Tamhane, 1987). The false discovery rate (FDR) controlling method of Benjamini and Hochberg (Benjamini and Hochberg, 1995) provides weak control of the FWER, and controls the FDR below level α. The FDR is defined as the expected proportion of incorrect rejections of H0, relative to the total number of rejections. The significance level α= 0.05 was chosen for this study.
Submission date Jul 28, 2007
Last update date Aug 14, 2011
Contact name Misook Ha
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 GPL5680
Series (1)
GSE9513 Duplicate genes increase expression diversity in closely related species and allopolyploids

Data table header descriptions
Fold_change (A.thaliana)/(A.arenosa)
VALUE Log e ( Fold_change)
STD Standard deviation of signal
P-value_pergene Significance of intensity difference between two samples in pergene varicance model
P-value_common_gene Significance of intensity difference between two samples in common gene variance model

Data table
ID_REF Fold_change VALUE STD P-value_pergene P-value_common_gene
A001457_01 0.7157 -0.33449 0.53367 0.011473 0.20388
A021520_01 1.0528 0.051453 0.74102 0.3322 0.84505
A010714_01 1.0258 0.025435 0.61206 0.83933 0.92303
A018176_01 0.83516 -0.18013 0.67767 0.06371 0.49383
A008034_01 0.90085 -0.10441 0.47192 0.16968 0.69165
A006550_01 0.87659 -0.13171 0.53293 0.16587 0.61686
A000682_01 0.83483 -0.18053 0.55616 0.05275 0.49288
A023921_01 1.7744 0.57348 0.66694 2.90E-05 0.02938
A013064_01 0.88512 -0.12203 0.58065 0.15623 0.64299
A012903_01 1.0868 0.083267 0.73075 0.58362 0.75178
A024662_01 3.4848 1.2484 0.6863 0.00089022 2.12E-06
A020054_01 0.97585 -0.024444 0.50597 0.59309 0.92602
A024893_01 0.97677 -0.023502 0.42656 0.5167 0.92887
A016958_01 0.71124 -0.34074 0.80481 0.006173 0.19557
A024665_01 1.0521 0.050801 0.89697 0.46962 0.84699
A024791_01 1.0882 0.084568 0.72082 0.23763 0.74804
A018236_01 1.8532 0.61692 0.4999 0.00074418 0.019113
A017031_01 1.1844 0.16923 0.59735 0.0087397 0.52034
A003085_01 1.1178 0.1114 0.54029 0.19164 0.6722
A015355_01 0.92487 -0.078107 0.4943 0.66776 0.76671

Total number of rows: 26090

Table truncated, full table size 1325 Kbytes.

Supplementary file Size Download File type/resource
GSM213692_#19-at2-Cy3vscare_Cy5.gpr.gz 2.7 Mb (ftp)(http) GPR
GSM213692_#20-at2-Cy5vscare_Cy3.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM213692_#35-at2-Cy3vscare_Cy5.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM213692_#36-at2-Cy5vscare_Cy3.gpr.gz 2.7 Mb (ftp)(http) GPR
GSM213692_#37-at2-Cy3vscare_Cy5.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM213692_#38-at2-Cy5vscare_Cy3.gpr.gz 2.7 Mb (ftp)(http) GPR
GSM213692_#8-at2-Cy5vscare_Cy3.gpr.gz 2.6 Mb (ftp)(http) GPR
GSM213692_#9-at2-Cy3vscare_Cy5.gpr.gz 2.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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