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Probing Brachyury Function during ES cell differentiaiton

ABSTRACT: To probe how Brachyury regulates its target genes, we performed mRNA-seq to analyze gene expression changes after Brachyury depletion by the lentivirus-mediated shRNA

ORGANISM(S): Mus musculus

PROVIDER: GSE54984 | GEO | 2014/03/10

SECONDARY ACCESSION(S): PRJNA238202

REPOSITORIES: GEO

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Probing Brachyury Function during ES cell differentiaiton

Project description:To probe how Brachyury regulates its target genes, we performed mRNA-seq to analyze gene expression changes after Brachyury depletion by the lentivirus-mediated shRNA WT and Brachytury Knockdown embryoid bodies were collected at EB day 4. Subsequently, mRNA-seq expriments were performed with whole embryoid bodies

2014-03-10 | E-GEOD-54984 | biostudies-arrayexpress

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Project description:To identify Brachyury target genes in vivo and elucidate how Brachyury-mediated regulation contributes to early mouse developmental homeostasis and coordination, we performed mRNA-seq to compare gene expression profiles of WT and Tc/Tc embryos at both E7.5 ~ 8.0 and E10.0 ~ 10.5 WT and Tc/Tc embryos were isolated at both E7.5 ~ 8.0 and E10.0 ~ 10.5. Subsequently, directional mRNA-seq expriments were performed with wild-type and Tc/Tc whole embryos

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Project description:Brachyury (or T) is expressed in the primitive streak, tailbud and notochord of the early mouse embryo (Herrmann et al., 1990; Wilkinson et al., 1990). It plays a key role in early development: mouse embryos lacking functional Brachyury protein fail to gastrulate properly, do not form a differentiated notochord, and lack structures posterior to somite seven (Chesley, 1935; DobrovolskaM-CM-/a-ZavadskaM-CM-/a, 1927; Naiche et al., 2005; Wilson et al., 1995; Wilson et al., 1993; Yanagisawa et al., 1981) We apply a ChIP-on-chip approach to identify targets of Brachyury during mouse ES cell differentiation. ES cells provide an abundant source of differentiating cells and the identification of Brachyury targets in such cells will shed light on the mechanisms of ES cell differentiation and, by analyzing the targets in the developing embryo, will reveal to what extent they provide a bone fide model of early mouse development. The brachyury IP expts used 3 independent biological replicates hybridised to design 1 and 2 chips per replicate Design 1 raw file AE_251471610189 + Design 2 raw file AE_251471710182 = replicate 1 Design 1 raw file AE_251471610716 + Design 2 raw file AE_251471710724 = replicate 2 Design 1 raw file AE_251471610717 + Design 2 raw file AE_251471710725 = replicate 3 in all cases IP DNA label was Cy5 and whole chromatin Cy3 Design 1 files GSM417692 Design 2 files GSM417704 Isotype control experiment performed 1 x ie design 1 raw file AE_251471610714 design 2 raw file AE_251471710722 in GSM417714 and GSM417756 IP DNA label was Cy5 and whole chromatin Cy3 as for brachyury data

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