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Series GSE10877 Query DataSets for GSE10877
Status Public on Apr 21, 2008
Title Highly integrated single base resolution maps of the epigenome in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by genome tiling array
Methylation profiling by array
Methylation profiling by high throughput sequencing
Summary Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.

Understanding the epigenetic regulatory mechanisms that mediate control of transcription at multiple levels is critical to understanding how plants develop and respond to their environment. We combined next-generation sequencing by synthesis (SBS) technology with novel methods for direct sequencing of the entire cytosine methylome (methylC-seq), transcriptome (RNA-seq), and the small RNA component of the transcriptome (smRNA-seq) to create a set of highly integrated epigenome maps for Arabidopsis thaliana, in conjunction with a set of informative mutants defective in DNA methyltransferase and DNA demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and found that local composition has effects upon DNA methylation state. Deep sequencing of the smRNAome exposed a direct relationship between the location and abundance of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in the region of RNA-DNA homology. Finally, strand-specific RNA-seq revealed changes in the transcript abundance of hundreds of genes upon alteration of the DNA methylation state, and enabled the identification of numerous previously unidentified genes regulated by DNA methylation.

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.
 
Contributor(s) Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR
Citation(s) 18423832
Submission date Mar 18, 2008
Last update date May 15, 2019
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
 
Platforms (2)
GPL9062 Illumina Genome Analyzer (Arabidopsis thaliana)
GPL10977 [At35b_MR] Affymetrix Arabidopsis Tiling 1.0R Array
Samples (16)
GSM275647 col-0_mcip_1
GSM275648 col-0_mcip_2
GSM275649 col-0_no_antibody_1
This SuperSeries is composed of the following SubSeries:
GSE10966 Highly integrated epigenome maps in Arabidopsis - whole genome shotgun bisulfite sequencing
GSE10967 Highly integrated epigenome maps in Arabidopsis - small RNA sequencing
GSE10968 Highly integrated epigenome maps in Arabidopsis - transcriptome sequencing
Relations
BioProject PRJNA107265

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10877_RAW.tar 2.7 Gb (http)(custom) TAR (of CEL, TXT)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data provided as supplementary file

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