|
| Status |
Public on Apr 21, 2008 |
| Title |
col-0_mcip_1 |
| Sample type |
genomic |
| |
|
| Source name |
Immature floral tissue, unopened buds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Columbia-0
|
| Treatment protocol |
no treatment
|
| Growth protocol |
All plants were grown in potting soil (Metro Mix 250; Grace-Sierra, Boca Raton, FL) at 23˚C under a 16-hour light/8-hour dark cycle.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the immature floral tissue following instructions from the manufacturer (Qiagen, DNeasy Plant mini kit). Genomic DNA containing methylcytosines was immunoprecipitated with anti-5-methylcytosine antibody from 2 µg of fragmented genomic DNA.
|
| Label |
biotin
|
| Label protocol |
Immunoprecipitated genomic DNA was amplified using the Sigma GenomePlex WGA1 kit as per manufacturer's instructions to yield 15 µg, fragmented by incubation with DNaseI (0.05 U/µg DNA) for 10 min at room temperature, then denatured. DNA was labeled by incubating the fragmented DNA with biotin-16-dUTP, biotin-16-ddUTP and terminal transferase for 90 min at 37˚C.
|
| |
|
| Hybridization protocol |
The Arabidopsis Tiling 1.0R whole genome tiling array was hybridized for 16 h, washed and stained with a streptavidin-phycoerythrin conjugate on the Affymetrix Fluidics Station 450 accordingto the standard Affymetrix protocol.
|
| Scan protocol |
GeneChips were scanned on Affymetrix Scanner G7
|
| Description |
Col-0 methylcytosine immunoprecipitation replicate 1
|
| Data processing |
Gene chip data files were processed using TileMap to identify methylated regions, with a cutoff of 0.5 pp. The no antibody arrays were used as controls for identification of methylated regions.
|
| |
|
| Submission date |
Mar 18, 2008 |
| Last update date |
Sep 24, 2010 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL10977 |
| Series (2) |
| GSE10877 |
Highly integrated single base resolution maps of the epigenome in Arabidopsis |
| GSE10969 |
Highly integrated epigenome maps in Arabidopsis - methylcytosine immunoprecipitation |
|
