Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression profiling of Noto-GFP+ notochord progenitor cells sorted from E8.5 mouse embryos

ABSTRACT: Using a combination of cell sorting and microarray analysis, we identified almost 200 genes as having a high level of expression in the notochord. After whole mount in situ hybridization screening, we confirmed approximately one third of these as having a novel notochord expression pattern. Keywords: cell type comparison - embryonic Noto-GFP+ notochord progenitors versus surrounding GFP- comparator cells

ORGANISM(S): Mus musculus

PROVIDER: GSE14211 | GEO | 2011/10/01

SECONDARY ACCESSION(S): PRJNA111337

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression profiling of Noto-GFP+ notochord progenitor cells sorted from E8.5 mouse embryos

Project description:Using a combination of cell sorting and microarray analysis, we identified almost 200 genes as having a high level of expression in the notochord. After whole mount in situ hybridization screening, we confirmed approximately one third of these as having a novel notochord expression pattern. Keywords: cell type comparison - embryonic Noto-GFP+ notochord progenitors versus surrounding GFP- comparator cells 3 biological replicates - each replicate includes an experiment cell population (Noto-GFP positive cell sort) and a comparator population (GFP negative cell sort)

2011-09-30 | E-GEOD-14211 | biostudies-arrayexpress

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

The Ciona notochord transcriptome reveals a core set of broadly conserved notochord effector genes

Project description:The notochord is the eponymous feature of the chordates and an essential organ in chordate development. The notochord of the invertebrate chordate Ciona consists of only 40 cells, and is a longstanding model for studying differentiation and morphogenesis in a small, simple embryo. Here we perform RNAseq analysis on flow-sorted notochord cells from multiple stages of development to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression in the notochord and extensively validate the results by in situ hybridization. This notochord gene set is highly enriched for Gene Ontology codes related to the extracellular matrix, cell adhesion and cytoskeleton, and contains numerous genes with intriguing potential functions in morphogenesis. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as would be predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about the evolution of the notochord.

2017-09-19 | GSE95333 | GEO

RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

Project description:RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

| PRJNA544322 | ENA

Transcription profiling of Xenopus laevis developing notochord

Project description:We screened for differentially expressed genes in the developing notochord using the Affymetrix microarray system in Xenopus laevis. At late gastrula, we dissected four regions from the embryo, anterior mesoderm, posterior mesoderm, notochord and presomitic mesoderm. Three types of comparison were carried out to generate a list of predominantly notochord expressed genes: (1) Posterior mesoderm vs. anterior mesoderm; notochord genes are expected to be increased since the notochord is located in the posterior mesoderm. (2) Posterior mesoderm vs. whole embryos; notochord genes are expected to be increased. (3) Notochord vs. somite. This comparison sub-divided the group of posterior mesodermal genes identified in (1) and (2). All tissues are dissected using tungsten needles. We first dissected dorsal tissue above the archenteron from late gastrula to early neurula. To loosen tissue, we treated the dissected dorsal explant in a 1% cysteine solution (pH 7.4) and removed the neuroectodermal layer. Anterior mesoderm was dissected corresponding to about the anterior one-third of the archenteron roof, and the rest was collected as posterior mesoderm. The posterior mesodermal explant was dissected into notochord and somites, following a clearly visible border between the two tissues. The accuracy of all dissection was confirmed by RT-PCR of marker genes.

2006-12-31 | E-MEXP-717 | biostudies-arrayexpress

Differential gene expression in notochord and nerve-cord fate segregation in the Ciona intestinalis embryo

Project description:Fertilized eggs are plulipotent and during early embryogenesis, embryonic cells gradually restrict their developmental potential and are eventually destined to give rise to one type of cells. Molecular mechanism underlying developmental fate restriction is one of the major research subjects of developmental biology. Here we address this question by combining a classical technique of blastomere isolation with a modern technique of microarray analysis. During the 6th cleavage of the Ciona intestinalis embryo, from the 32-cell to the 64-cell stage, four mother cells divide into daughter cells with two distinct fates, one giving rise to notochord and the other to nerve-cord precursor cells. Nearly 500 notochord or nerve-cord precursor cells each were isolated, and difference in the quality of mRNAs between them was compared by microarray. This analysis identified 111 and 69 genes that are differentially expressed in the notochord and nerve-cord precursor cells, respectively. These included not only genes for transcription factors and signalling molecules but also those with functions that many kinds of cells used. In addition, whole-mount in situ hybridization showed complex and dynamic profiles of spatial expression of these genes during the segregation of the two fates. The process is accomplished by that transcripts that have been already present in the mother cell are properly partitioned into either type of cells and that new and preferential expression of genes in either type of cells. Two kinds of sample, Dye Swap design with 2 arrays

2014-02-01 | E-GEOD-25184 | biostudies-arrayexpress

Mus musculus

Project description:Expression profiling of Noto-GFP+ notochord progenitor cells sorted from E8.5 mouse embryos

| PRJNA111337 | ENA

Expression profiling of Ciona intestinalis initial tailbud stage embryos expressing mutant forms of the transcription factor Ci-XBP1 in the notochord.

Project description:XBP transcription factors are well-known regulators of the the unfolded protein response and are required for plasma cell differentiation. However, recent studies have shown that the XBP1 gene is also expressed in the developing notochord of Ciona and various vertebrates, and to date its role in the formation of this organ is largely uncharacterized. We identified putative targets of Ci-XBP1 through a microarray screen, using RNAs extracted from embryos expressing mutant forms of this transcriptional regulator in the notochord. We expressed in the Ciona notochord a dominant-negative version of Ci-XBP1 (XBP DBD::GFP) by cloning its DNA-binding domain (DBD) downstream of the Ci-Brachyury (Ci-Bra) promoter. We created a constitutive activator form of Ci-XBP by fusing its DBD to the VP16 transactivation domain (Bra>XBP DBD::VP16::GFP). These constructs were introduced into 1-cell stage embryos and grown to the initial tailbud (iTb) stage to identify Ci-XBP notochord target genes.

2022-01-20 | GSE46751 | GEO

Sorted MDMs with RFP+GFP+ or RFP+GFP- Mtb

Project description:Sorted MDMs with RFP+GFP+ or RFP+GFP- Mtb

| PRJNA542934 | ENA

Expression data from chordoma and notochord (microarray)

Project description:Chordoma is a rare malignant tumor thought to originate from embryonic notochord. However, no molecular comparison of chordoma and notochord has been performed to date, leaving the identities of dysregulated pathways unclear. Absence of a molecular description of a control tissue clouds our understanding of chordoma. Thus, we conducted an unbiased comparison of chordoma and notochord using gene expression profiling to clarify chordoma’s tissue of origin and identify novel drug targets

2023-02-07 | GSE224776 | 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