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SRX8844290: GSM4700181: VN_rep3 [RNA-seq]; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 18.9M spots, 945.8M bases, 354.8Mb downloads

Submitted by: NCBI (GEO)
Study: Epigenetic reprogramming events rewire transcription during the alternation of generations in Arabidopsis [RNA-Seq]
show Abstracthide Abstract
Alternation between morphologically distinct haploid and diploid life forms is a defining feature of most plant and algal life cycles, yet the underlying molecular mechanisms that govern these transitions remain unclear. Here, we explore the dynamic relationship between chromatin accessibility and epigenetic modifications during life form transitions in Arabidopsis. The diploid-to-haploid life form transition is governed by the loss of H3K9me2 and DNA demethylation of transposon-associated cis-regulatory elements, which is associated with dramatic changes in chromatin accessibility and transcriptional reprogramming. In contrast, the global loss of H3K27me3 in the haploid form shapes a chromatin accessibility landscape that is poised to re-initiate the transition back to diploid life after fertilization. These distinct epigenetic reprogramming events rewire transcription through major reorganization of the regulatory epigenome to guide the alternation of generations in flowering plants. Overall design: Gene expression profiling of VN and dme-2/+ mutant pollen.
Sample: VN_rep3 [RNA-seq]
SAMN15667723 • SRS7107177 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: For analysis of dme-2/+ pollen, dry pollen was harvested from Col-gl and BASTA-sprayed dme-2/+ plants using a method published previously. Pollen grains were disrupted in a Precellys tissue homogenizer (Bertin Instruments) and total RNA isolated using an RNeasy Micro Kit (Qiagen). For vegetative cell nuclei, FACS-isolated nuclei from the ProVCK:NTF line were sorted directly into Trizol reagent and precipitated with isopropanol. RNA-seq libraries were generated from the resulting RNA with Smart-seq2 using independent biological replicates. The libraries were sequenced on an Illumina Hiseq 2500 using 50 bp paired-end and single-end reads for VN and pollen samples, respectively.
Experiment attributes:
GEO Accession: GSM4700181
Links:
Runs: 1 run, 18.9M spots, 945.8M bases, 354.8Mb
Run# of Spots# of BasesSizePublished
SRR1234460018,916,855945.8M354.8Mb2021-01-26

ID:
11500879

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