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Series GSE1356 Query DataSets for GSE1356
Status Public on Jun 12, 2004
Title Histone methylation in wild type and ddm1 Arabidopsis thaliana seedlings
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Histone 3 lysine 4 and histone 3 lysine 9 methylation in wild type and ddm1 Arabidopsis thaliana seedlings. 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.

This SuperSeries is composed of the SubSeries listed below.
Overall design Refer to individual Series
Contributor(s) Vaughn MW
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Submission date Apr 30, 2004
Last update date Dec 28, 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 (16)
GSM21801 EV49, Wild-type seedlings H3mK4
GSM21802 EV50, Wild-type seedlings H3mK4
GSM21804 EV55, ddm1 seedlings H3mK4
This SuperSeries is composed of the following SubSeries:
GSE1333 EV49+50, Histone 3 Lysine 4 methylation in wild-type Arabidopsis thaliana seedlings
GSE1334 Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings
GSE1335 EV104+105, Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings
BioProject PRJNA90107

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Supplementary data files not provided

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