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Series GSE80300 Query DataSets for GSE80300
Status Public on Jun 24, 2016
Title A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation using whole-genome bisulfite sequencing
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary The non-methylable cytosine analogs, 5-azacytidine and zebularine, are widely used to disrupt DNA methyltransferase activity and reduce genomic DNA methylation. In this study, whole-genome bisulfite sequencing is used to construct maps of DNA methylation with single base pair resolution in Arabidopsis thaliana seedlings treated with each demethylating agent. We find that 5-azacytidine and zebularine-treated seedlings have nearly indistinguishable patterns of DNA methylation genome-wide and that 5-azacytidine, despite being more unstable in aqueous solution, has a slightly greater demethylating effect at higher concentrations across the genome. Transcriptome analyses revealed a substantial number of up-regulated genes and transposable element genes, particularly CACTA-like elements, demonstrating that chemical demethylating agents have a disproportionately large effect on loci that are silenced by DNA methylation.
Overall design Bisulfite-Seq and RNA-Seq
Contributor(s) Schmitz RJ
Citation(s) 27402357
Submission date Apr 14, 2016
Last update date May 15, 2019
Contact name Robert J Schmitz
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (15)
GSM2123995 Untreated_control
GSM2123996 Mock_control
GSM2123997 AZA_25
BioProject PRJNA318516
SRA SRP073326

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Supplementary file Size Download File type/resource
GSE80300_RAW.tar 1.4 Gb (http)(custom) TAR (of TSV)
GSE80300_gene_exp.diff.gz 1.1 Mb (ftp)(http) DIFF
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Raw data are available in SRA
Processed data provided as supplementary file

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