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SRX277579: GSM1139912: DNaseI-seq 0d biological replicate 1; Arabidopsis thaliana; DNase-Hypersensitivity
8 ILLUMINA (Illumina HiSeq 2000) runs: 166.6M spots, 8.5G bases, 4.8Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Developmental dynamics of DNA accessibility during flower development [DNaseI-Seq]
show Abstracthide Abstract
Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programmes. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood. Here, we characterize the dynamic relationship of chromatin accessibility, gene expression and DNA-binding of two MADS-domain proteins during Arabidopsis flower development. The developmental dynamics of DNA-binding of APETALA1 and SEPALLATA3 is largely independent of chromatin accessibility, and our findings suggest that AP1 acts as ‘pioneer factor’ that modulates chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes. Our data provide a primer to the idea that cellular differentiation in plants can be associated to dynamic changes in chromatin accessibility, as consequence of the action of master transcription factors. Overall design: We used the AP1-GR system to conduct DNaseI hypersensitivity experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. As control, naked DNA from wild-type inflorescences was used. Experiments were done in two biological replicates. The GSE47981 includes expression data that are complementary to the data in the GSE46986 and GSE46894.
Sample: DNaseI-seq 0d biological reps 1 and 2
SAMN02143032 • SRS420692 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: DNase-Hypersensitivity
Source: GENOMIC
Selection: DNase
Layout: SINGLE
Construction protocol: Nuclei isolation from 0.2 g of plant material was performed according to (Zhang et al., 2007) and DNA digestion was performed according (Hesselberth et al., 2009). Two biological replicates for each time point were sequenced on Illumina HighSeq2000. Libraries were prepared using the Illumina according to manufacture's instructions of the sample prep kit from Illumina
Experiment attributes:
GEO Accession: GSM1139912
Links:
External link:
Runs: 8 runs, 166.6M spots, 8.5G bases, 4.8Gb
Run# of Spots# of BasesSizePublished
SRR85051220,504,7531G590Mb2014-02-03
SRR85051324,121,5021.2G712.5Mb2014-02-03
SRR85051427,383,9251.4G813.9Mb2014-02-03
SRR85051529,902,8241.5G914.5Mb2014-02-03
SRR85051613,016,141663.8M375Mb2014-02-03
SRR85051715,261,478778.3M451.6Mb2014-02-03
SRR85051817,391,954887M517.9Mb2014-02-03
SRR85051919,001,547969.1M582.6Mb2014-02-03

ID:
394489

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