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Series GSE52400 Query DataSets for GSE52400
Status Public on Dec 17, 2014
Title BABY BOOM (BBM) ChIP-seq in Arabidopsis somatic embryo tissue
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Horstman A, Muino JM, Boutilier K
Citation(s) 25564655
Submission date Nov 14, 2013
Last update date May 15, 2019
Contact name Kim Boutilier
E-mail(s) kim.boutilier@wur.nl
Organization name Plant Research International
Street address Droevendaalsesteeg 1
City Wageningen
ZIP/Postal code 6708 PB
Country Netherlands
 
Platforms (1)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
Samples (4)
GSM1264686 pBBM::BBM-YFP
GSM1264687 pBBM::NLS-GFP
GSM1264688 35S::BBM-GFP
Relations
BioProject PRJNA227780
SRA SRP033014

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52400_35SL003vsL004bg2_t2.wig.gz 54.9 Mb (ftp)(http) WIG
GSE52400_pBBMBBMYFPvsNLSbg2_t2.wig.gz 32.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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