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Series GSE63463 Query DataSets for GSE63463
Status Public on Oct 11, 2015
Title Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq]
Platform organism Arabidopsis lyrata
Sample organisms Arabidopsis thaliana; Arabidopsis lyrata
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression.
Overall design Chromatin was crosslinked and isolated from wildtype A. lyrata inflorescences up to floral stage 10/11. The immunoprecipitation of protein-DNA complexes was performed using a peptide SEP3 antibody that was raised against A. thaliana SEP3, and is also able to recognize the homolog from A. lyrata due to protein similarity. As a control, de-crosslinked 'input-DNA' was used. SEP3 ChIP-seq on Arabidopsis thaliana can be found in the accessions GSM364939 and GSM364941. Re-analyzed peak positions for these samples are included as a supplementary file on the series level (SEP3Ratiobg5@TAIR10-win.csv).
Contributor(s) Muino JM, de Bruijn S, Vingron M, Angenent GC, Kaufmann K
Citation(s) 26429922
Submission date Nov 19, 2014
Last update date May 15, 2019
Contact name Jose M. Muino
Organization name Humboldt University
Department Department of Biology
Street address Rhoda-⁠Erdmann-⁠Haus (Haus 22); R 1216 Philippstr. 11-⁠13;
City Berlin
ZIP/Postal code 10115
Country Germany
Platforms (2)
GPL19447 Illumina HiSeq 2000 (Arabidopsis lyrata)
GPL20223 Illumina MiSeq (Arabidopsis lyrata)
Samples (3)
GSM1550360 lySEP3-biorep1
GSM1550362 InputDNA-biorep1
GSM1691851 lySEP3-biorep2
This SubSeries is part of SuperSeries:
GSE63464 Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor
Reanalysis of GSM364939
Reanalysis of GSM364941
BioProject PRJNA267854
SRA SRP050052

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
GSE63463_RAW.tar 2.6 Mb (http)(custom) TAR (of CSV)
GSE63463_SEP3Ratiobg5_TAIR10-win.csv.gz 230.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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