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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional targets of Xenopus EBF3 in the presence 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. 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

ORGANISM(S): Xenopus laevis

SUBMITTER: Monica Vetter

PROVIDER: E-GEOD-25734 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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EBF factors drive expression of multiple classes of target genes governing neuronal development.

Green Yangsook S YS Vetter Monica L ML

Neural development 20110430

<h4>Background</h4>Early B cell factor (EBF) family members are transcription factors known to have important roles in several aspects of vertebrate neurogenesis, including commitment, migration and differentiation. Knowledge of how EBF family members contribute to neurogenesis is limited by a lack of detailed understanding of genes that are transcriptionally regulated by these factors.<h4>Results</h4>We performed a microarray screen in Xenopus animal caps to search for targets of EBF transcript ...[more]

PMID: 21529371

Similar Datasets

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.

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.

2011-05-25 | GSE27084 | GEO

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

Multicilin drives centriole biogenesis via E2f proteins

Project description:Biochemistry suggests e2f4 forms a complex with the coiled-coiled protein multicilin (MCIDAS), a protein that is necessary and sufficient to specify multiciliated cells in vertebrates. Here, we performed RNAseq on Xenopus laevis ectoderm in the presence of multicilin alone or multicilin and a dominant-negative e2f4 construct. We also performed ChIPseq on e2f4 in the presence or absence of multicilin. Taken together, these data demonstrate how multicilin affects e2f4 genomic targets and their downstream transcription. RNAseq: misexpression of multicilin-HGR +/- dominant-negative e2f4 messenger RNAs in X. laevis animal caps, multicilin induced with dexamethasone at mid-stage 11 and harvested at 3 timepoints (3, 6, and 9 hours after induction, roughly corresponding to stages 13, 16, and 18) with 3 biological replicates. ChIPseq: misexpression of e2f4-GFP +/- multicilin-HGR messenger RNAs in X. laevis animal caps, multicilin induced at mid-stage 11 and harvested at one timepoint (6 hours after induction, roughly corresponding to stage 16), immunoprecipitated with anti-GFP and sequenced; 2 biological replicates. Background was input prior to IP.

2014-07-10 | E-GEOD-59309 | biostudies-arrayexpress

Multicilin promotes centriole assembly and ciliogenesis during multiciliate cell differentiation.

Project description:Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) alone, to block the formation of multiciliate cells, or with Dexamethasone inducible Multicilin (MCI-HGR) to induce the formation of ectopic multiciliate cells. MCI-HGR plus ICD injected samples were compared to ICD alone to identify candidate genes whose expression changes when MCI is active. Epithelial cells projecting hundreds of motile cilia are prominent in the respiratory system, brain ependyma and female reproductive tract where they generate a vigorous fluid flow along luminal surfaces. Despite their importance for organ function, how multiciliate cells arise developmentally in diverse epithelia is poorly understood. We identified a novel coiled-coil protein, we have termed multicilin (MCI), whose expression is Notch regulated and restricted to epithelia where multiciliate cells form in Xenopus embryos. In order to identify early downstream targets of multicilin we blocked the formation of endogenous multiciliate cells by injecting ICD mRNA. In a subset of samples we then misexpressed a dexamethasone inducible form of MCI (MCI-HGR) to identify specific targets of MCI in explants of Xenopus epithelium. In explants expressing MCI-HGR genes specifically expressed in ciliated cells such as FoxJ1 and alpha-tubulin were highly upregulated along with various genes known to be required for ciliogenesis, and a large number of genes likely to be part of the ciliome based on homology of potential structural motifs. 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD or ICD along with MCI-HGR. At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip. At stage 11.5 dexamethasone was added to all conditions to induce MCI. Explants were harvested 5 hours after adding dexamethasone (approximately stage14) and used as the starting material for arrays.

2012-03-01 | E-GEOD-32452 | biostudies-arrayexpress

Occupancy and transcriptional profile of Prdm12 in posteriorized neural tissue

Project description:V1 interneurons are a class of inhibitory neurons that play an essential role in vertebrate locomotion; however, the factors contributing to their specification are poorly understood. Morphological and molecular evidence suggest that the zinc finger transcription factor Prdm12 may play a role in promoting V1 interneurons while repressing V2 and V0 fates. Here, we performed RNAseq on Xenopus laevis ectoderm converted to posteriorized neural tissue (with noggin and retinoic acid) in the presence or absence of a series of Prdm12 constructs (wild-type Prdm12, Prdm12-VP16, and Prdm12-engrailed-repressor). We also performed ChIPseq on a Prdm12-FLAG in wild-type or posteriorized neuralized (with noggin and retinoic acid) X. laevis ectoderm. Taken together, these data demonstrate Prdm12's genomic targets and their downstream transcription. X. laevis embryos were injected with mRNAs encoding prdm12 constructs, along with the bmp inhibitor noggin. Presumptive ectoderm (neuralized by noggin) was dissected and treated with retinoic acid. Samples were then processed into RNAseq libraries or prdm12-FLAG was immunoprecipitated and its targets sequenced. Background was input prior to IP.

2015-11-04 | E-GEOD-64551 | biostudies-arrayexpress

Histone modification and transcription factor ChIPseq of Xenopus laevis epithelial progenitors

Project description:To determine the positions of promoters and enhancers in developing Xenopus laevis epithelial progenitors, we performed ChIPseq on the histone modifications H3K4me3 and H3K27ac. We also performed ChIPseq on the transcription factors foxj1 (in the presence or absence of rfx2), myb (in the presence or absence of multicilin), and rad21. Some embryos were harvested as wild-types; in other experiments, we injected embryos with mRNAs encoding FLAG-foxj1 (with and without rfx2 morpholino) or GFP-myb (with and without an inducible form of multicilin (mcidas-HGR)). We then isolated epithelial progenitors surgically and, when injected with multicilin, induced at mid-stage 11. We then harvested chromatin at 9 hours after induction (roughly stage 18) and performed ChIPseq using antibodies against endogenous targets (H3K4me3, H3K27ac, rad21) or protein tags (FLAG, GFP). We then sequenced these libraries, aligned the reads to the X. laevis genome (version 9.1) with bwa mem and called peaks with HOMER, using input as background.

2016-02-23 | E-GEOD-78176 | biostudies-arrayexpress

Identification of microRNAs and microRNA targets in Xenopus ectoderm

Project description:Purpose: The establishment of cell lineages occurs via a dynamic progression of gene regulatory networks that underlie developmental commitment and differentiation. To investigate how microRNAs (miRs) function in this process, we compared miRs and miR targets at the initiation of the two major ectodermal lineages in Xenopus. Methods: We injected Xenopus laevis embryos with noggin or constitutively active BMP4 receptor (CABR) at two-cell stage and cut animal caps at stg. 8. Isolated animal caps were grown separately till mid gastrula and processed for either RNA isolation or immunoprecipitation. Results: We have identified over 400 miRNAs in early neural and epidermal ectoderm. The Ago-RNP RNAs from these tissues represent overlapping, yet distinct, subsets of genes. Moreover, the profile of Ago-RNP associated genes differs substantially from the profile of total RNAs in these tissues. Identification of microRNAs and microRNA targets in establishment of early ectodermal tissues in Xenopus.

2016-06-28 | E-GEOD-83784 | biostudies-arrayexpress

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

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