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SRX647774: GSM1429897: RGA_ChIP1; Arabidopsis thaliana; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 31.2M spots, 1.6G bases, 1.1Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: RGA binding sites in Arabidopsis thaliana seedlings
show Abstracthide Abstract
DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis. Overall design: Provided are 3 biological replicates analysing RGA binding sites in Arabidopsis seedlings. ChIP-seq was performed on plants expressing RGA-GFP under the native RGA promoter and on non-transgenic control plants as reference
Sample: RGA_ChIP1
SAMN02904825 • SRS655043 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Selection: ChIP
Layout: SINGLE
Construction protocol: Fixation of the plant material and ChIP was performed as described in Gendrel, et al. 2005, (Nature Methods, 2(3), 213–8). Nuclear extracts were split in two and incubated each with 20 µl of GFP-Trap_A (ChromoTek) for 4 h at 5°C for immunoprecipitation. MinElute Reaction Cleanup Kit columns (Qiagen) were used for purification of the DNA fragments. Sequencing libraries were generated using pooled DNA from each 7 to 10 individual ChIP preparations of either RGA-GFP or WT material. Libraries were prepared for Illumina Sequencing using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240) with the NEBNext Multiplex Oligos for Illumina (E7335 and E7500). Libraries were quantified using the Qubit Fluorometer from Invitrogen, and their size determined using the DNA 1000 Assay on the BioAnalyzer. Sequencing was performed on the Illumina HiSeq 2000 Instrument 50 base SE (plus index read).
Experiment attributes:
GEO Accession: GSM1429897
External link:
Runs: 1 run, 31.2M spots, 1.6G bases, 1.1Gb
Run# of Spots# of BasesSizePublished


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