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Series GSE63462 Query DataSets for GSE63462
Status Public on Oct 11, 2015
Title Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]
Organisms Arabidopsis thaliana; Arabidopsis lyrata
Experiment type Expression 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 RNA-seq libraries were generated from 3 tissues: A. lyrata leaves, A. lyrata inflorescences, and A.thaliana inflorescences. 3 biological replicates were sequenced.
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)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL19447 Illumina HiSeq 2000 (Arabidopsis lyrata)
Samples (9)
GSM1550351 lyleaves rep1
GSM1550352 lyleaves rep2
GSM1550353 lyleaves rep3
This SubSeries is part of SuperSeries:
GSE63464 Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor
BioProject PRJNA267853
SRA SRP050051

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
GSE63462_RAW.tar 1.0 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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