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The Xenopus animal cap transcriptome: building a mucociliary epithelium.

ABSTRACT: The Xenopus animal cap transcriptome: building a mucociliary epithelium.

PROVIDER: PRJNA436118 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6786720_1.fastq.gz	Fastqsanger.gz
	SRR6786720_2.fastq.gz	Fastqsanger.gz
	SRR6786721_1.fastq.gz	Fastqsanger.gz
	SRR6786721_2.fastq.gz	Fastqsanger.gz
	SRR6786722_1.fastq.gz	Fastqsanger.gz

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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

Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

Project description:This study was conducted to investigate the effects of DN-tp63 loss-of-function on mucociliary basal stem cells in Xenopus laevis. Uninjected control embryos and DN-tp63 morpholino oligonucleotide injected embryos were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16-19, and 24-25 for total RNA extraction.

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The Xenopus animal cap transcriptome: building a mucociliary epithelium.

Project description:With the availability of deep RNA sequencing, model organisms such as Xenopus offer an outstanding opportunity to investigate the genetic basis of vertebrate organ formation from its embryonic beginnings. Here we investigate dynamics of the RNA landscape during formation of the Xenopus tropicalis larval epidermis. Differentiation of non-neural ectoderm starts at gastrulation and takes about one day to produce a functional mucociliary epithelium, highly related to the one in human airways. To obtain RNA expression data, uncontaminated by non-epidermal tissues of the embryo, we use prospective ectodermal explants called Animal Caps (ACs), which differentiate autonomously into a ciliated epidermis. Their global transcriptome is investigated at three key timepoints, with a cumulative sequencing depth of ?108 reads per developmental stage. This database is provided as online Web Tool to the scientific community. In this paper, we report on global changes in gene expression, an unanticipated diversity of mRNA splicing isoforms, expression patterns of repetitive DNA Elements, and the complexity of circular RNAs during this process. Computationally we derive transcription factor hubs from this data set, which may help in the future to define novel genetic drivers of epidermal differentiation in vertebrates.

| S-EPMC6158741 | biostudies-literature

Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

Project description:Mucociliary epidermis RNA-seq data from comparison of controls and DN-tp63 morpholino knockdown in Xenopus animal cap explants.

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Development of Xenopus Mucociliary Epithelium

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Transcription profiling of Xenopus animal cap cardiogenesis model to examine immediate early targets of Gata4 and Gata5.

Project description:Gata factors are amongst the genes expressed early on in the process of cardiogenesis. We used microarrays to examine the immediate early targets of Gata4 and Gata5 in the Xenopus leavis animal cap cardiogenesis model. We hope to use these data to examine the roles of Gata4 and Gata5 in cardiogenesis and also to begin to dissect out the common and distinct targets of Gata4 and Gata5. Experiment Overall Design: Xenopus leavis embryos were injected at the one cell stage with dexamethasone-inducible Gata4 or Gata5 mRNA constructs (to examine endodermal and mesodermal targets) or with Gata4 in the presence of Dkk1 (to examine mesodermal targets.) Embryos were cultured to stage 9, whereupon animal caps were excised and cultured for 2.5 hours in media containing dexamethasone to induce the constructs and cycloheximide to block de novo protein synthesis and thus give only immediate early targets.

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A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating - RNA DIF-FRAC Xenopus laevis Animal Cap explants Replicate 1

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Xenopus laevis animal cap explants with and without RNAse A treatment.

2020-03-10 | PXD017659 | Pride

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating - RNA DIF-FRAC Xenopus laevis Animal Cap explants Replicate 2

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Xenopus laevis animal cap explants with and without RNAse A treatment.

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Mucociliary epidermis RNA-seq data from controls and after manipulation of cell fates by Notch (suh-dbm, nicd) and cell type controlers (Foxa1MO, dnMCIDAS)

Project description:This study was conducted to investigate the effects of enriching or depleting cell types in mucociliary organoids in Xenopus laevis. (1) Uninjected control embryos were compared to (2) inhibition of Notch signaling (suh-dbm) which enriches ionocytes and multiciliated cells, (3) inhibition of Notch and suppression of MCIDAS (suh-dbm + dnMCIDAS) which enriches ionocytes and depletes multiciliated cells, (4) overactivation of Notch (nicd) which suppresses ionocytes and multiciliated cells and promotes small secretory cells and basal cells, (5) knockdown of foxa1 (foxa1MO) which depletes small secretory cells. Embryos were injected at 2-4 cell stage and were used to generate animal cap explants at embryonic stage 8. Explants were grown into mucociliary organoids and collected at embryonic stages 10.5, 16, 25, and 32 for total RNA extraction.

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Microarray analysis of Xenopus tRNA isoacceptor families, RNA Polymerase III target genes and selected mRNAs in control and fgf4/wnt8 induced animal cap explants at NF stage 25

Project description:Animal poles of 1 to 2-cell stage embryos were injected with a cocktail containing 5pg of Fgf4 and 50pg wnt8 mRNA. Embryos were grown alongside batch controls to NF stage 8/9. Animal cap explants were dissected from the embryos and grown overnight in NAM alongside whole embryo controls as a means of staging. At NF stage 25, caps were collected for microarray analysis. Custom microarrays containing sequences for Xenopus tRNA and RNA Polymerase III gene families as well as selected mRNAs were used to detect changes in transcription at this stage in response to induction of myogenic differentiation. We aimed to use this data to investigate the relationship between any codon bias in highly expressed mRNAs with expression of their matching tRNA isoacceptors in response to a specific differentiation programme.

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