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Series GSE51048 Query DataSets for GSE51048
Status Public on Nov 27, 2013
Title Regulatory Modules Controlling Maize Inflorescence Architecture: ChIP-seq data
Organism Zea mays
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary In this study we investigated the developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, and revealed potential mechanisms for repressing branches in distinct stem cell populations in developing maize inflorescences. To identify targets of RA1 and to distinguish direct vs. indirect interactions, we performed Chromatin Immunoprecipitation (ChIP)-seq and compared the results to gene expression data (RNA-seq datasets for Eveland et al., 2013, submitted). We mapped genome-wide occupancy of RA1 and showed that it differently regulates modules of target genes based on spatiotemporal context.
 
Overall design Plants expressing complementing RA1 transgenes tagged with HA or YFP were used in parallel experiments. Ear and tassel primordia were collected and tag-specific antibodies were used to pull down RA1 bound to its target loci. Genome-wide analysis of RA1 occupancy revealed thousands of putative binding sites (i.e. peaks significantly enriched (p < 1e-05) compared to input DNA).
 
Contributor(s) Eveland AL, Jackson DP, Ware D, Pautler M, Morohashi K, Grotewold E, Vollbrecht EW
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Submission date Sep 20, 2013
Last update date May 15, 2019
Contact name Andrea L Eveland
E-mail(s) aeveland@danforthcenter.org
Organization name Donald Danforth Plant Science Center
Street address 975 N. Warson Road
City St. Louis
State/province MO
ZIP/Postal code 63132
Country USA
 
Platforms (2)
GPL9361 Illumina Genome Analyzer II (Zea mays)
GPL15463 Illumina HiSeq 2000 (Zea mays)
Samples (8)
GSM1236536 RA1_ChIPseq_tassel_HA
GSM1236537 RA1_ChIPseq_tassel_YFP
GSM1236538 RA1_input_tassel_HA
This SubSeries is part of SuperSeries:
GSE51050 Regulatory Modules Controlling Maize Inflorescence Architecture
Relations
BioProject PRJNA219748
SRA SRP030122

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
GSE51048_RAW.tar 700.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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