|
Status |
Public on Apr 21, 2008 |
Title |
col-0_no_antibody_2 |
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). 2 µg of fragmented genomic DNA was incubated under the same conditions as the methylcytosine immunoprecipitation samples, except no antibody was added.
|
Label |
biotin
|
Label protocol |
Genomic DNA from the "no antibody" control 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 control (no antibody) replicate 2
|
Data processing |
Gene chip data files were processed using TileMap. This array was one of two control samples that were used to identify methylated regions in the methylcytosine immunoprecipitation reactions.
|
|
|
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 |
|