Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Probing In vivo Brachyury Function with Tc mouse model

ABSTRACT: 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

ORGANISM(S): Mus musculus

SUBMITTER: Zhe Liu

PROVIDER: E-GEOD-54982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Probing In vivo Brachyury Function with Tc mouse model

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

2014-03-10 | GSE54982 | GEO

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

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

2014-03-10 | GSE54984 | GEO

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

Project description: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.

2017-10-01 | GSE94142 | GEO

Escovopsis sp. TC strain:TC

Project description:Escovopsis sp. TC strain:TC Genome sequencing and assembly

| PRJNA388866 | ENA

Alicyclobacillus sp. TC strain:TC

Project description:Alicyclobacillus sp. TC strain:TC Genome sequencing and assembly

| PRJNA562382 | ENA

Transcriptome of thyroid cancer (TC) cells after coculture with TC-induced macrophages

Project description:RNA sequencing data of TPC-1 cells (TC cell line) after co-culture with TC-induced macrophages. We used an in vitro co-culture model of a human TC cell line, TPC1 (RET/PTC rearrangement), and human primary monocytes.

2020-09-21 | GSE120391 | GEO

Ectopic expression of the Brachyury transcription factor upregulates only a subset of notochord expressed genes

Project description:The key notochord transcription factor Brachyury was ectopically expressed in Ciona embryos under the control of the FoxAa cis-regulatory region (which drives expression in neural, endodermal and mesenchymal lineages in addition to notochord). Misexpression of Brachyury induced 925 genes compared to a control reporter plasmid (Bra>GFP). There was only modest overlap with a set of notochord-enriched genes previously identified by RNAseq of flow-sorted notochord cells, indicating that Brachyury is not a notochord master regulator gene as strictly defined.

2017-09-19 | GSE102142 | GEO

Targets of the transcription factor Brachyury in differentiating mouse ES cells

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; 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. 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.

2012-05-29 | GSE16646 | GEO

Genome wide chromatin changes in TC-32 and TC-71 Ewing sarcoma cell lines.

Project description:We performed ChIPseq on histone modification marks, transcriptional factors and chromatin architectural proteins in TC-32 and TC-71 Ewing sarcoma cell lines.

2019-08-07 | GSE115250 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data