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| 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
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| 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.
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| Overall design |
Refer to individual Series
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| Contributor(s) |
Vaughn MW |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Apr 30, 2004 |
| Last update date |
Dec 28, 2012 |
| Contact name |
Matthew Wayne Vaughn |
| E-mail(s) |
vaughn@tacc.utexas.edu
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| Phone |
(512) 232-7124
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| Organization name |
University of Texas at Austin
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| Department |
Texas Advanced Computing Center
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| Lab |
Vaughn
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| Street address |
10100 Burnet Rd
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78758 |
| Country |
USA |
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| Platforms (1) |
| GPL785 |
Arabidopsis thaliana (ecotype Columbia) chromosome 4 knob genomic tiling array |
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| Samples (16)
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| GSM21805 |
EV56, ddm1 seedlings H3mK4 |
| GSM21807 |
EV104, ddm1 seedlings H3mK4 |
| GSM21808 |
EV105, ddm1 seedlings H3mK4 |
| GSM21810 |
EV106, WT seedlings H3mK4 |
| GSM21811 |
EV107, WT seedlings H3mK4 |
| GSM21813 |
EV51, Wild-type seedlings H3mK9 |
| GSM21814 |
EV52, Wild-type seedlings H3mK9 |
| GSM21816 |
EV59, ddm1 seedlings H3mK9 |
| GSM21817 |
EV60, ddm1 seedlings H3mK9 |
| GSM21819 |
EV108, Wild-type seedlings H3mK9 |
| GSM21820 |
EV109, Wild-type seedlings H3mK9 |
| GSM21822 |
EV110, ddm1 seedlings H3mK9 |
| GSM21823 |
EV111, ddm1 seedlings H3mK9 |
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| This SuperSeries is composed of the following SubSeries:
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| 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 |
| GSE1336 |
Ev106+107, Histone 3 Lysine 4 methylation in WT Arabidopsis thaliana seedlings |
| GSE1337 |
EV51+52, Histone 3 Lysine 9 methylation in wild-type Arabidopsis thaliana seedlings |
| GSE1338 |
EV59+60, Histone 3 Lysine 9 methylation in ddm1 Arabidopsis thaliana seedlings |
| GSE1339 |
Histone 3 Lysine 9 methylation in wild-type Arabidopsis thaliana seedlings |
| GSE1340 |
EV110+111, Histone 3 Lysine 9 methylation in ddm1 Arabidopsis thaliana seedlings |
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| Relations |
| BioProject |
PRJNA90107 |
| Supplementary data files not provided |
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