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SRX377734: GSM1264686: pBBM::BBM-YFP; Arabidopsis thaliana; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 223.6M spots, 11.4G bases, 7Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: BABY BOOM (BBM) ChIP-seq in Arabidopsis somatic embryo tissue
show Abstracthide Abstract
After fertilization, a plant's life relies on progression through embryogenesis and maintenance of the stem cell niches from which all post-embryonic organs arise. BABY BOOM (BBM) and other members of the AINTEGUMENTA-LIKE (AIL)/PLETHORA (PLT) clade of the AP2-type transcription factor family play important roles controlling these processes in Arabidopsis thaliana (Arabidopsis). Development of the plt2/bbm double mutant is blocked at during early embryogenesis (Galinha et al., 2007), and combinations of bbm with plt1 and plt3 lead to short roots as a result of meristem differentiation. In contrast, overexpression of BBM in Arabidopsis seedlings induces the formation of somatic embryos on cotyledons and leaves (Boutilier, 2002), showing that BBM is a key regulator of cell identity and proliferation. Although the functions of BBM and other AIL genes have been well described, the molecular mode of action of these transcription factors has not been well examined (reviewed in Horstman et al., 2013). Our previous study provided the first insight into BBM molecular function by identifying BBM targets through a microarray-based approach (Passarinho, 2008), but only a few BBM targets have been functionally characterized. To obtain a better understanding of BBM function, we identified direct BBM targets using a chromatin immunoprecipitation (ChIP) combined with massively-parallel DNA sequencing (ChIP-seq) approach. Overall design: Somatic embryo tissue was used for the ChIP-seq experiments with the native BBM promoter (pBBM::BBM-YFP), with a line expressing nuclear-localized GFP from the same BBM promoter (pBBM::NLS-GFP) as a negative control. Whole, embryogenic seedlings of the 35S::BBM-GFP line were used for the 35S::BBM-GFP ChIP-seq experiments, with 35S::BBM embryogenic seedlings serving as a negative control. Both experiments were performed once, making a total of 4 samples.
Sample: pBBM::BBM-YFP
SAMN02402787 • SRS502541 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: ChIP-Seq
Selection: ChIP
Layout: SINGLE
Construction protocol: Somatic embryo material was cross-linked using formaldehyde and ground prior to nuclear extraction. The nuclear pellet was sonicated and the lysate was used for immunoprecipitation with the µMACS GFP Isolation Kit (Miltenyi). After proteinase K treatment, the DNA was purified using the QIAquick kit (Qiagen). The Illumina ChIP-Seq library preparation kit was used for library construction using the manufacturer's protocol, except that 1:10 dilutions were used of the adapters. Library fragments of 200-500 bp were excised from the gel and purified.
Experiment attributes:
GEO Accession: GSM1264686
External link:
Runs: 1 run, 223.6M spots, 11.4G bases, 7Gb
Run# of Spots# of BasesSizePublished


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