GSM5350729: Col-H3K27me3-24h_rep2; Arabidopsis thaliana; ChIP-Seq - SRA

SRX11037826: GSM5350729: Col-H3K27me3-24h_rep2; Arabidopsis thaliana; ChIP-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 18M spots, 5.4G bases, 1.7Gb downloads

Submitted by: NCBI (GEO)

Study: A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis [H3K27me3 ChIP-seq]

PRJNA704828 • SRP308163 • All experiments • All runs

show Abstracthide Abstract

We report transcriptome changes and genome-wide dynamics of H3K27me3 during seed germination in Arabidopdsis, and investigate the impact of REF6-mediated H3K27 demethylation on germination. Compared with transcriptome changes, we discover delayed H3K27me3 reprogramming closely associated with the embryo to vegetative cell fate switch. REF6-mediated H3K27 demethylation promotes germination but does not significantly contribute to H3K27me3 dynamics during germination, but rather stably establishes an H3K27me3-depleted state permissive to transcription. By analyzing REF6 genomic binding, we show that it is absent from mature embryo chromatin and gradually establishes occupancy during the course of germination to counteract increased PRC2 activity. Overall design: Examination of transcriptome, H3K27me3 and REF6 binding in germinating seeds and seedlings

Sample: Col-H3K27me3-24h_rep2

SAMN19486937 • SRS9107237 • All experiments • All runs

Organism: Arabidopsis thaliana

Library:

Instrument: Illumina NovaSeq 6000

Strategy: ChIP-Seq

Source: GENOMIC

Selection: ChIP

Layout: PAIRED

Construction protocol: Materials were ground with liquid nitrogen into fine powder and fixed with 1% formaldehyde. To profile H3K27me3, nuclei were extracted and mononucleosomes were generated with micrococcal nuclease (MNase)(Sigma, N5386) digestion. Immunoprecipitation was conducted with anti-H3K27me3 antibody (Merck, 07-449). After antibody incubation, Protein A Dynabeads (Life technologies, 10002D) were added to collect the immunocomplexes, followed by elution, reverse cross-linking and DNA purification. Library was prepared with VAHTS universal DNA library prep kit for illumina (Vazyme, ND607) according to the manufacture's instruction

Experiment attributes:

GEO Accession: GSM5350729

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 18M spots, 5.4G bases, 1.7Gb

Run	# of Spots	# of Bases	Size	Published
SRR14699747	18,049,406	5.4G	1.7Gb	2022-11-10

ID:: 14684086

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity