GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE1334 Query DataSets for GSE1334
Status Public on Jun 12, 2004
Title Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype. This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3. In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. 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.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled only by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Ddm1 seedlings, 9 days old
This is the normalized result of the paired dye swap samples EV55 and EV56.
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 false discovery rate (FDR) controlling methods. 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 after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K4 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate method were used to analyze this sample.
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
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)
GSM21804 EV55, ddm1 seedlings H3mK4
GSM21805 EV56, ddm1 seedlings H3mK4
This SubSeries is part of SuperSeries:
GSE1356 Histone methylation in wild type and ddm1 Arabidopsis thaliana seedlings
BioProject PRJNA91045

Normalized result of the paired dye swap samples EV55 and EV56 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
pc01a01F.1000.4.1200143.T10P11_1 1.19530008008511 0.19733 0.18768 0 0
pc01a02F.999.4.1201129.T10P11_1 1.56700513977686 0.13235 0.0012477 0 1
pc01a03F.1009.4.1202124.T10P11_1 1.60074274463351 1.086 0.33445 0 0
pc01a04F.1019.4.1203243.T10P11_1 2.00577663671374 0.067452 2.1067e-10 0 1
pc01a05F.1002.4.1204327.T10P11_1 0.565323082141444 0.13566 0.00016914 0 1
pc01a06F.923.4.1205524.T10P11_1 2.07520544533909 0.1704 0.00013857 0 1
pc01a07F.967.4.1206542.T10P11_1 0.980776775205963 0.77106 0.49008 0 0
pc01a08F.995.4.1207488.T10P11_1 1.80661945367828 0.15599 0.00047128 0 1
pc01a09F.1001.4.1208553.T10P11_1 1.42736836095291 0.36212 0.168 0 0
pc01a10F.978.4.1209635.T5J8_1 1.24350269840086 1.183 0.42773 0 0
pc01a11F.1031.4.1210591.T5J8_1 0.698324022346369 0.52379 0.24991 0 0
pc01a12F.855.4.1211906.T5J8_1 1.37500515626934 1.5671 0.42038 0 0
pc01b01F.991.4.1212715.T5J8_1 1.13809664716728 0.78969 0.43566 0 0
pc01b02F.980.4.1213666.T5J8_1 0.868130914141853 0.33535 0.33862 0 0
pc01b03F.972.4.1214603.T5J8_1 0.94197437829691 0.72111 0.4673 0 0
pc01b04F.986.4.1215711.T5J8_1 1.53029213276815 0.22548 0.035929 0 0
pc01b05F.990.4.1216676.T5J8_1 1.14383757506434 0.5013 0.39551 0 0
pc01b06F.984.4.1217785.T5J8_1 1.00803403122889 0.12183 0.4741 0 0
pc01b07F.949.4.1218748.T5J8_1 2.97115013221618 0.27354 0.00029491 0 1
pc01b08F.977.4.1219676.T5J8_1 1.3284623048821 0.19703 0.081451 0 0

Total number of rows: 1724

Table truncated, full table size 116 Kbytes.

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap