Pluto Bioinformatics

GSE94142: Genome wide maps of H3K4me3, H3K27me3 and H3K27ac in Brachyury mutants and RNA-seq data of Brachyury mutants

Bulk RNA sequencing

The transcription factor BRACHYURY is the founding member of the T-box family of proteins. A conserved residue (Y88 in BRACHYURY) was previously suggested to be important for interaction with KDM proteins that demethylate H3K27me3. We generated Brachyury mutant mouse embryonic stem cell (ESC) lines. For a wild type control (Thet) we derived an embryonic stem cell line from blastocysts, containing a single wild type copy of the Brachyury locus (T +/2J; 2J is a large genomic deletion of the entire Brachyury locus). We mutated the remaining wild type copy of Brachyury to code for Alanin instead of the conserved tyrosine (Y88) residue (T_Y88A). We derived embryos from these ESCs, compare expression profiles (RNAseq) from Thet and TY88A caudal end mesoderm of early embryos (stages: TS12 and TS13), and complement the expression data with histone methylation ChIPseq data for H3K4me3, HeK27me3 and H3K27ac. Of note: due to the different requirements of cellular material for RNAseq and ChIPseq we differentiated the same ESC used for the embryo generation (in vivo, RNA-seq) to generate early caudal end mesoderm in vitro (ChIPseq). In addition, this dataset contains a ChIPseq track for BRACHURY in wild type ESCs, differentiated into early mesoderm in vitro with the same protocol as for the histone ChiIPseq. SOURCE: Phillip Grote (grote@med.uni-frankfurt.de) - Grote Goethe University