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Transcriptional targets of Xenopus EBF3 in the absence of Noggin : Untreated animal caps vs. Dexamethasone (DEX) treated animal caps

ABSTRACT: Transcriptional profiling comparing the genes upregulated or downregulated by active hGR-Xebf3 by treating hormone DEX to those by non-active hGR-Xebf3 in Xenopus animal caps.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE27084 | GEO | 2011/05/25

SECONDARY ACCESSION(S): PRJNA137475

REPOSITORIES: GEO

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Transcriptional targets of Xenopus EBF3 in the presence of Noggin : Untreated animal caps vs. Dexamethasone (DEX) treated animal caps

Project description:Transcriptional profiling comparing the genes upregulated or downregulated by active hGR-Xebf3 by treating hormone DEX to those by non-active hGR-Xebf3 in Xenopus animal caps.

2011-05-25 | GSE25734 | GEO

Transcriptional targets of Xenopus EBF3 in the absence of Noggin : Untreated animal caps vs. Dexamethasone (DEX) treated animal caps

Project description:Transcriptional profiling comparing the genes upregulated or downregulated by active hGR-Xebf3 by treating hormone DEX to those by non-active hGR-Xebf3 in Xenopus animal caps. Three experimental conditions, hGR-Xebf3 without DEX treatment (1), hGR-Xebf3 with DEX treatment (2), and hGR with DEX treatment (3). Comparison, 1 vs.2 and 1 vs. 3. Biological replicate, one time

2011-05-25 | E-GEOD-27084 | biostudies-arrayexpress

Transcriptional targets of Xenopus EBF3 in the presence of Noggin : Untreated animal caps vs. Dexamethasone (DEX) treated animal caps

Project description:Transcriptional profiling comparing the genes upregulated or downregulated by active hGR-Xebf3 by treating hormone DEX to those by non-active hGR-Xebf3 in Xenopus animal caps. Three experimental conditions, Noggin and hGR-Xebf3 without DEX treatment (1), Noggin and hGR-Xebf3 with DEX treatment (2), and Noggin and hGR with DEX treatment (3). Comparison, 1 vs.2 and 1 vs. 3. Biological replicates, 4 times

2011-05-25 | E-GEOD-25734 | biostudies-arrayexpress

Transcriptional profiling of Xenopus laevis animal caps overexpressing MyoD

Project description:mRNa encoding for XtMyoD was overexpressed in animal caps and the transcriptional profile of uninjected and injected animal caps was compared.

2011-06-22 | E-MEXP-3273 | biostudies-arrayexpress

Xenopus laevis embryos and animal caps: Control vs PouV morpholino

2013-11-12 | GSE47578 | GEO

Xenopus laevis embryos and animal caps: Control vs PouV morpholino

Project description:Transcriptional profiling of Xenopus laevis embryos and ectoderm (animal caps) comparing embryos injected with control morpholino with embryos injected with the morpholino mixture PVD2, which knocks down all three Xenopus PouV proteins. Whole embryos (WE) or animal caps (AC) were collected at late blastula (9) or early gastrula (10) stages from Control and PVD2 morphants. Two conditions: Control vs. PouV morpholino; Two tissues: whole embryos, animal caps .Two timepoints: stage 9 and 10. Biological replicates: 2 control replicates at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps, 2 PVD2 morpholino replicates at stage 9 and 10 for whole embryos, 2 control replicates at stage 9 and 10 for animal caps

2013-11-12 | E-GEOD-47578 | biostudies-arrayexpress

Endoderm induction by the organizer-secreted factors chordin and noggin in Xenopus animal caps.

Project description:Spemann's organizer has potent neural inducing and mesoderm dorsalizing activities in the Xenopus gastrula. A third activity, the organizer's ability to induce a secondary gut, has been difficult to analyze experimentally due to the lack of early gene markers. Here we introduce endodermin, a pan-endodermal gene marker, and use it to demonstrate that chordin (Chd), a protein secreted by the organizer region, is able to induce endodermal differentiation in Xenopus. The ability of chd, as well as that of noggin, to induce endoderm in animal cap explants is repressed by the ventralizing factor BMP-4. When FGF signaling is blocked by a dominant-negative FGF receptor in chd-injected animal caps, neural induction is inhibited and most of the explant is induced to become endoderm. The results suggest that proteins secreted by the organizer, acting together with known peptide growth factors, regulate differentiation of the endodermal germ layer.

| S-EPMC452184 | biostudies-other

Identification of Kctd15 target genes in Xenopus animal caps injected with wnt3a and chordin

Project description:We aimed to identify genes that are inhibited by Kctd15 overexpression during neural crest (NC) induction. Injection of RNAs encoding Wnt3a and chordin into the embryo followed by animal cap explant culture leads to the induction of NC marker genes as well as additional genes expressed in the neural plate border. Our previous study indicated that co-injection of kctd15 inhibits the induction of these markers. We injected four sets of RNAs, lacZ as control (L), wnt3a+chd (WC), wnt3a+chd+kctd15 (WCK), and kctd15 (K). After evaluation of marker gene expression with RT-PCR, we prepared probes with same RNA extract for Affymetrix DNA microarray. The hybridization, washing and scanning were perfomed following the manual from Affymetrix. Partek Genomics Suite was employed for data analysis. Xenopus embryos were injected with mRNAs at two-cell stage. When developing to stage 9, the animal caps were dissected for RNA extraction and hybridization on Affymetrix microarrays. According to the mRNAs injected, the animal caps (AC) were divided into four groups, including (1) AC injected with lacZ; (2) AC injected with kctd15; (3) AC injected with chordin and wnt3a; (4) AC injected with chordin, wnt3a and kctd15. The injected animal caps were cultured till stage 15 and then collected for RT-PCR and microarray assay. Each group had three repeats.

2015-08-26 | E-GEOD-72391 | biostudies-arrayexpress

Xenopus laevis kidney-induced animal caps nanoLC-MS/MS - Xenopus Ssbp2 is required for embryonic pronephros morphogenesis and terminal differentiation.

Project description:The nephron, functional unit of the vertebrate kidney, is specialized in metabolic wastes excretion and body fluids osmoregulation. Given the high evolutionary conservation of gene expression and segmentation patterning between mammalian and amphibian nephrons, the Xenopus laevis pronephric kidney offers a simplified model for studying nephrogenesis. The Lhx1 transcription factor plays critical roles in kidney development, regulating target gene expression by forming multiprotein complexes with LIM binding protein 1 (Ldb1). However, few Lhx1-Ldb1 cofactors have been identified for this organ formation. By tandem- affinity purification from kidney-induced Xenopus animal caps, we identified single-stranded DNA binding protein 2 (Ssbp2) to interact with the Ldb1-Lhx1 complex. Ssbp2 is expressed in the Xenopus pronephros, and knockdown prevents normal morphogenesis and differentiation of the glomus and the convoluted renal tubules. We demonstrate a role for a member of the Ssbp family in kidney organogenesis and provide evidence of a fundamental function for the Ldb1-Lhx1-Ssbp transcriptional complexes in embryonic development.

2023-10-24 | PXD041761 | Pride

Genome wide analysis of Suv4-20h1/2 depleted animal caps [dataset2]

Project description:Suv4-20h1/2 are histone methyltransferases that write the H4K20me2 and H4K20me3 marks. We knocked down these enzymes using translation blocking morpholinos in X. tropicalis animal caps and performed RNA-seq in order to investigate the impact of altering H4K20me state on epidermal differentiation. Knocking down Suv4-20h1/2 leads to a strong increase of H4K20me1 in bulk chromatin. To determine whether increased H4K20me1 is responsible for transcriptional changes in suv4-20h KD animal caps, we performed RNA-Seq for a rescue experiment with PHF8, an H4K20me1 demethylase.

2021-09-01 | GSE161248 | GEO

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