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SRX2804487: GSM2616968: RNAseq WT floral bud plant 2; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 32.8M spots, 1.7G bases, 825.5Mb downloads

Submitted by: NCBI (GEO)
Study: Comparative Epigenomics Reveals Hierarchical Regulation of Non-CG Methylation in Arabidopsis
show Abstracthide Abstract
Background: Genome-wide characterization by next-generation sequencing has greatly improved our understanding of the “landscape” of epigenetic modifications. Since 2008, whole-genome bisulfite sequencing (WGBS) has become the gold standard for DNA methylation analysis and a tremendous amount of WGBS data has been generated by the research community. However, methods for the systematic comparison of DNA methylation profiles to identify novel regulatory mechanisms have yet to be established.Results: Here we developed a standardized pipeline and re-analyzed over three hundred publicly available Arabidopsis WGBS libraries from various mutant backgrounds, tissue types, and stress treatments. In total this collection included more than 3,700 Gb (Giga base-pairs) of sequencing data and a large number of wild-type controls. This enabled us to identify “high-confidence Differentially Methylated Regions” (hcDMRs) with high reliability by comparing each 'test' library to each of the 54 controls. We adopted two statistical methods, Statistical Measurements on Overlapping of DMRs (S-MOD) followed by Quantitative Measurements on Overlapping of DMRs (Q-MOD), to compare and cluster libraries based on their impacts on DNA methylation. In addition to confirming existing relationships using this unbiased approach, we revealed novel connections between methylation pathways. For instance, MET1 and CMT3 were found to be required for maintenance of asymmetric CHH methylation at non-overlapping regions of CMT2 targeted heterochromatin.Conclusions: Our comparative methylome approach has established a framework for extracting biological insights via large-scale comparison of methylomes, and can also be adopted for other omics datasets. Together, the results demonstrate the effectiveness of data-driven, hypothesis-generating epigenetic research. Overall design: this dataset includes 7 RNA-seq and 1 BS-seq libraries
Sample: RNAseq WT floral bud plant 2
SAMN06958423 • SRS2184671 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Direct-zol RNA miniprep kit (#R2050) including in-column DNase treatment Each library is from a separate plant. 75ng total RNA was used as input for the TruSeq Stranded mRNA Library Prep Kit for Neoprep (NP-202-1001)
Experiment attributes:
GEO Accession: GSM2616968
Links:
Runs: 1 run, 32.8M spots, 1.7G bases, 825.5Mb
Run# of Spots# of BasesSizePublished
SRR553488232,788,9241.7G825.5Mb2018-01-02

ID:
4039215

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