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SRX1669856: GSM2101454: Columella root cap RNA-seq; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 66.8M spots, 3.4G bases, 2.3Gb downloads

Submitted by: NCBI (GEO)
Study: Unique cell-type specific patterns of DNA methylation in the root meristem (RNA-seq)
show Abstracthide Abstract
DNA methylation is an epigenetic modification that differs between plant organs and tissues, but the extent of variation between cell types is not known. Here, we report single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and small RNA transcriptomes for six cell populations covering the major cell types of the Arabidopsis root meristem. We identify widespread cell type specific patterns of DNA methylation, especially in the CHH sequence context. The genome of the columella root cap is the most highly methylated Arabidopsis cell characterized to date. It is hypermethylated within transposable elements, accompanied by increased abundance of transcripts encoding RNA-directed DNA methylation (RdDM) pathway components and 24 nt small RNAs. Absence of the nucleosome remodeler DECREASED DNA METHYLATION 1, required for maintenance of DNA methylation, and low abundance of histone transcripts involved in heterochromatin formation suggests a loss of heterochromatin may occur in the columella, thus allowing access of RdDM factors to the whole genome, and producing excess 24 nt small RNAs in this tissue. Together, these maps provide new insights into the epigenomic diversity that exists between distinct plant somatic cell types. Overall design: RNA-seq from six cell populations covering the major cell types of the Arabidopsis root meristem.
Sample: Columella root cap RNA-seq
SAMN04590211 • SRS1367618 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: Fluorescent Activated Cell Sorting (FACS) was performed using cell specific GFP lines. Sorted cells were collected directly into specific lysis buffers that were compatible with downstream applications. Cells used for bisulfite sequencing, mRNA-seq, smRNA-seq were lysed in Buffer AP1 (Qiagen), Buffer RLT (Qiagen), Trizol (Invitrogen). All samples were immediately stored at -80 °C until gDNA and RNA was extracted using DNeasy Plant mini kit (Qiagen) and RNeasy Plant mini kit (Qiagen) or Trizol, respectively. RNA-seq library preparation was performed using the Illumina TruSeq RNA Library Prep kit from polyA+ selected mRNA as per manufacturer’s instructions.
Experiment attributes:
GEO Accession: GSM2101454
Runs: 1 run, 66.8M spots, 3.4G bases, 2.3Gb
Run# of Spots# of BasesSizePublished


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