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Sample GSM275648 Query DataSets for GSM275648
Status Public on Apr 21, 2008
Title col-0_mcip_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). 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 2
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
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

Supplementary file Size Download File type/resource
GSM275648.CEL.gz 41.5 Mb (ftp)(http) CEL
GSM275648.txt.gz 56.9 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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