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Identification of microRNAs and microRNA targets in Xenopus ectoderm

ABSTRACT: 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.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE83784 | GEO | 2016/06/28

SECONDARY ACCESSION(S): PRJNA326974

REPOSITORIES: GEO

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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

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

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

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Transcription profiling of Xenopus embryos

Project description:Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays. Experiment Overall Design: Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays.

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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

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Project description:Xenopus laevis RNA-Seq on animal caps

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EFTF vs GFP Experiment

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The Xenopus animal cap transcriptome: building a mucociliary epithelium.

Project description:Here we investigate dynamics of the RNA landscape during formation of the Xenopus tropicalis larval epidermis. To obtain RNA expression data, we used ectodermal explants (Animal Caps), which differentiate autonomously into a ciliated epidermis, highly related to the one in human airways. Animal caps were harvested at the gastrula neurula and tailbud stage.

2018-09-25 | GSE111171 | GEO

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