GEO DataSets

(Submitter supplied) 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; Dobrovolskaïa-Zavadskaïa, 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. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4129 GPL4128

4 Samples

Download data: TXT

(Submitter supplied) UTX gene is localized on the X chromosome, identified as a demethylase on histone H3 lysine 27.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5465

Platform:

GPL1261

4 Samples

Download data: CEL

Analysis of embryonic stem cells lacking UTX. UTX is a histone H3K27 demethylase that belongs to the the family of JmjC domain-containing proteins. Results provide insight into the role of UTX in embryonic stem cell differentiation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE35415

4 Samples

Download data: CEL

(Submitter supplied) Genetic dissection of the mouse Brachyury locus identified a notochord enhancer and predicts additional control elements essential for trunk and tail development of the mouse embryo.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

1 Sample

Download data: BW

(Submitter supplied) Using chromatin immunoprecipitation combined with microarrays we have identified targets of No tail (Ntl), a zebrafish Brachyury ortholog that plays a central role in mesoderm formation. We show that Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl binding site that resembles the consensus T-box binding site (TBS) previously identified by in vitro studies. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by genome tiling array

9 related Platforms

27 Samples

Download data: GPR

(Submitter supplied) 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). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: BW, XLSX

(Submitter supplied) The transcription factor BRACHYURY (T, BRA) is one of the first markers of gastrulation and lineage specification in mammals. Despite its wide use and importance in stem cell and developmental biology, its genomic targets are largely unknown. Here, we used differentiated human embryonic stem cells to study the role of BRA in Bmp4-induced mesoderm and Activin-induced endoderm progenitors by ChIP-seq. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

6 Samples

Download data: BED, BW

(Submitter supplied) Lysine specific demethylase 1 (LSD1), which demethylates mono- and di- methylated histone H3-Lys4 as part of a complex including CoREST and histone deacetylases (HDAC), is essential for embryonic development in the mouse beyond e6.5 days. Here, we demonstrate that LSD1 expression and therefore function, is restricted to the epiblast of the post- implantation embryo. Conditional deletion of LSD1 in mouse embryonic stem (ES) cells, in vitro counterpart of the epiblast, revealed a reduction in CoREST protein, a subsequent decrease in associated HDAC activity and a global increase in Histone H3 Lys56 acetylation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

6 Samples

Download data: TXT

(Submitter supplied) Oct4 is an essential regulator of embryonic stem (ES) cell pluripotency in vivo and in vitro, as well as a key mediator of the reprogramming of somatic cells to form induced pluriopotent stem (iPS) cells. It is not known whether activation and/or repression of specific genes by Oct4 is relevant to these functions. Here we show that fusion proteins containing the coding sequence of Oct4 or Xlpou91 (the Xenopus homologue of Oct4) fused to activating regions, but not those fused to repressing regions, behave as Oct4, suppressing differentiation and promoting maintenance of undifferentiated phenotypes in vivo and in vitro. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6867

18 Samples

Download data: TXT

(Submitter supplied) The Tbx factors Eomesodermin (Eomes) and Brachyury instruct endoderm and mesoderm specification. Both Tbx factors have common large overlap in chromatin binding sites, however their embryonic phenotypes of mutants largely differ. In this study, we delineate the distinct binding patterns and gene target sets of Eomes and Brachyury providing a molecular model of distinct fate specification programs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL24247

20 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) Despite being found in the notochord of several chordates, the roles of the Tbx2 subfamily of T-box transcription factors in the development of this tissue remain largely unknown. We explored the targets of the only Tbx2 subfamily member in Ciona intestinalis, Ci-Tbx2/3, by expressing mutant forms of the transcriptional regulator using the Ci-Bra promoter region. We produced a dominant interfering version of Ci-Tbx2/3 (Tbx2/3DBD) through expression of a truncated version consisting only of its DNA-binding domain (DBD) and a constitutive activator form by attaching the T-box of Ci-Tbx2/3 to the VP16 transactivation domain (Tbx2/3VP16). more...

Organism:

Ciona intestinalis

Type:

Expression profiling by array

Platform:

GPL15657

17 Samples

Download data: CEL

(Submitter supplied) ChIP-seq using anti-GFP antibody to map genomic binding of Prdm4-EGFP in stably transfected mouse embryonic stem cells

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BED, WIG

(Submitter supplied) Expression profiling of wild-type, Prdm4 null and Prdm4-EGFP overexpressing mouse embryonic stem cells using Illumina whole genome V2 arrays. The hypothesis tested was that Prdm4 regulates gene expression consistant with Prdm4 genomic binding identified by ChIP-seq

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23563 GPL29327

42 Samples

Download data

(Submitter supplied) The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. more...

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29327

15 Samples

Download data: XLSX

(Submitter supplied) The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. more...

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29327

12 Samples

Download data: XLSX

(Submitter supplied) The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. more...

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29327

6 Samples

Download data: XLSX

(Submitter supplied) The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona. Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes are unaffected by CRISPR Bra disruption. more...

Organism:

Ciona robusta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23563

9 Samples

Download data: XLSX

(Submitter supplied) In vertebrate embryos, anterior tissues are generated early, followed by the other axial structures that emerge sequentially from a posterior growth zone. The genetic network driving posterior axial elongation in mice, and its disturbance in mutants with posterior truncation are not yet fully understood. We show that the combined expression of Cdx2 and T Brachyury is essential to establish the core signature of posterior axial progenitors. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL19057

55 Samples

Download data: BED, BW, CSV, WIG

(Submitter supplied) Epiblast stem cells (EpiSC) are pluripotent stem cells derived from mouse postimplantation embryos between E5.5 to E7.5, a time window in which gastrulation commences. Therefore, EpiSC represent a valuable tool for studying mammalian postimplantation development in vitro. Beyond their pluripotent features, EpiSC can also be reprogrammed into a mouse embryonic stem cell-like (mESC) state. Published reports showed that EpiSC reversion requires transcription factor overexpression, while others suggest that applying stringent mESC culture conditions alone was sufficient to revert EpiSC to mESC-like cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

7 Samples

Download data: TXT