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Series GSE1330 Query DataSets for GSE1330
Status Public on Jun 12, 2004
Title DNA methylation in ddm1 seedling Arabidopsis thaliana plants
Organism Arabidopsis thaliana
Experiment type Methylation profiling by genome tiling array
Summary The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thaliana genotype.
McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment.
In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
ddm1 seedlings, 9 days old.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
This is the normalized result of the paired dye swap samples VC131 and VC135.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns.
Keywords: other
 
 
Contributor(s) Lippman ZB, Gendrel A, Black M, Vaughn MW
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 21, 2004
Last update date Mar 15, 2012
Contact name Matthew Wayne Vaughn
E-mail(s) vaughn@tacc.utexas.edu
Phone (512) 232-7124
Organization name University of Texas at Austin
Department Texas Advanced Computing Center
Lab Vaughn
Street address 10100 Burnet Rd
City Austin
State/province TX
ZIP/Postal code 78758
Country USA
 
Platforms (1)
GPL785 Arabidopsis thaliana (ecotype Columbia) chromosome 4 knob genomic tiling array
Samples (2)
GSM21792 VC131, ddm1 seedlings DNA methylation
GSM21793 VC135, ddm1 seedlings DNA methylation
This SubSeries is part of SuperSeries:
GSE1355 DNA methylation in Arabidopsis thaliana
Relations
BioProject PRJNA91037

Normalized result of the paired dye swap samples VC131 and VC135 header descriptions
ID_REF Feature name
VALUE Normalized value
STDERR Standard error for the feature
PVALUE P-value for the feature
FWER 1: Feature was found to be significant via Holm's method
FDR 1: Feature was found to be significant via Benjamini and Hochberg's step-up procedure

Data table
ID_REF VALUE STDERR PVALUE FWER FDR
pc01a01F.1000.4.1200143.T10P11_1 1.17008330993167 1.6155 0.46215 0 0
pc01a02F.999.4.1201129.T10P11_1 1.31971388602951 0.253 0.14508 0 0
pc01a03F.1009.4.1202124.T10P11_1 1.12038541258193 1.2678 0.46508 0 0
pc01a04F.1019.4.1203243.T10P11_1 1.08068385674455 0.21982 0.36449 0 0
pc01a05F.1002.4.1204327.T10P11_1 1.23120867755876 0.22625 0.18623 0 0
pc01a06F.923.4.1205524.T10P11_1 1.18718317049138 0.45979 0.35712 0 0
pc01a07F.967.4.1206542.T10P11_1 1.21555423195206 0.2142 0.18827 0 0
pc01a08F.995.4.1207488.T10P11_1 0.908595311648192 0.12434 0.22642 0 0
pc01a09F.1001.4.1208553.T10P11_1 1.14025085518814 0.21569 0.27597 0 0
pc01a10F.978.4.1209635.T5J8_1 1.3064381270903 1.8246 0.44274 0 0
pc01a11F.1031.4.1210591.T5J8_1 1.11630814570054 0.064303 0.053833 0 0
pc01a12F.855.4.1211906.T5J8_1 1.14276572159941 0.32909 0.34541 0 0
pc01b01F.991.4.1212715.T5J8_1 1.22482974866494 1.5838 0.44991 0 0
pc01b02F.980.4.1213666.T5J8_1 1.27331762908257 0.19659 0.11899 0 0
pc01b03F.972.4.1214603.T5J8_1 1.37266475408711 0.42559 0.2341 0 0
pc01b04F.986.4.1215711.T5J8_1 1.20161978346812 0.12939 0.0881 0 0
pc01b05F.990.4.1216676.T5J8_1 1.40708325711632 0.60119 0.2892 0 0
pc01b06F.984.4.1217785.T5J8_1 0.82014270483064 0.23765 0.20864 0 0
pc01b07F.949.4.1218748.T5J8_1 1.35725725454003 0.45353 0.25543 0 0
pc01b08F.977.4.1219676.T5J8_1 0.916338312104829 0.23204 0.35595 0 0

Total number of rows: 1722

Table truncated, full table size 114 Kbytes.




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