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E-GEOD-39780 - Zygotic gene activatory network in zebrafish is globally controlled by Pou5f1 SoxB1 enhancers

Status
Released on 10 August 2013, last updated on 3 May 2014
Organism
Danio rerio
Samples (4)
Protocols (8)
Description
Genetic control of pluripotent mammalian ES cells is determined by a transcriptional network, with a "central core" of transcription factors, Pou5f1, Sox2 and Nanog. Zebrafish homologues of the "core pluripotency factors" Pou5f1, SoxB1 and Nanog-like are also crucially involved in early development. However, the degree of functional similarity of the network between mammals and non-mammals is a matter of debate. To identify the components of Pou5f1-dependent transcriptional networks, we determined the genomic binding sites for Pou5f1 and Sox2 in late blastula stage zebrafish embryos using ChIP-seq. We found that Sox2 and Pou5f1 are co-binding to the regulatory regions of Sox2, Pou5f1, and Nanog-like, as well as to multiple orthologues of mammalian plutipotency network components. Deep sequencing was performed using the Illumina GAIIx on DNA samples obtained from Sox2 ChIP, Pou5f1-Flag ChIP and Input Control. Pou5f1 was analysed in technical duplicates to obtain higher sequencing depth.
Experiment type
ChIP-seq 
Contacts
Manuel Leichsenring <geo@ncbi.nlm.nih.gov>, Daria Onichtchouk, Julia Maes, Rebecca Mössner, Wolfgang Driever
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-39780.idf.txt
Sample and data relationshipE-GEOD-39780.sdrf.txt
Processed data (1)E-GEOD-39780.processed.1.zip
Links