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Series GSE43755 Query DataSets for GSE43755
Status Public on Dec 09, 2013
Title Expression data from early zebrafish embryos either untreated or treated with retinoic acid
Organism Danio rerio
Experiment type Expression profiling by array
Summary Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation. Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites. This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages. We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements. Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development.
 
Overall design Expression of embronic transcripts were used to determine expressed and non-expressed gene groups for further chromatin studies.
 
Contributor(s) Weicksel SE, Sagerstrom CG
Citation(s) 23671670
Submission date Jan 25, 2013
Last update date Jan 25, 2018
Contact name Steven Weicksel
E-mail(s) steven.weicksel@umassmed.edu
Organization name UMass Medical School
Department BMP
Lab Sagerstrom
Street address 55 Lake Ave
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (14)
GSM1070387 Untreated four hour post fertilization embryo rep 1
GSM1070388 Untreated four hour post fertilization embryo rep 2
GSM1070389 Untreated six hour post fertilization embryo rep 1
This SubSeries is part of SuperSeries:
GSE43758 Identification of nucleosome positions at hox TSSs during zebrafish early embryonic development
Relations
BioProject PRJNA187331

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
GSE43755_RAW.tar 27.8 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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