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RNA Seq analysis of E9.5 embryonic vagal regions in Rdh10 mutants of mouse

ABSTRACT: RNA Seq analysis of E9.5 embryonic vagal regions in Rdh10 mutants of mouse

PROVIDER: PRJNA701439 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13689555.fastq.gz	Fastqsanger.gz
	SRR13689556.fastq.gz	Fastqsanger.gz
	SRR13689557.fastq.gz	Fastqsanger.gz
	SRR13689558.fastq.gz	Fastqsanger.gz
	SRR13689559.fastq.gz	Fastqsanger.gz

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RNA Seq analysis of E9.5 embryonic vagal regions in Rdh10 mutants of mouse

Project description:The enteric nervous system (ENS) is formed from vagal neural crest cells (NCC), which generate the neurons and glia that regulate gastrointestinal function. Defects in the migration, colonization or differentiation of NCC in the gut can result in gastrointestinal disorders such as Hirschsprung disease (HSCR). Although mutations in many genes have been associated with the etiology of HSCR, a significant proportion of affected individuals have an unknown genetic diagnosis. Therefore, it’s important to identify new genes, modifiers and environmental factors that regulate ENS development and HSCR. We discovered that retinol dehydrogenase 10 (Rdh10) loss-of-function mouse embryos exhibit total intestinal aganglionosis, the most severe form of HSCR. Rdh10 catalyzes the first oxidative step in the metabolism of vitamin A to its active metabolite, RA, and is therefore a central regulator of vitamin A metabolism and retinoic acid (RA) synthesis during embryogenesis. Rdh10 is highly expressed in the mesenchyme surrounding the entrance to the foregut and we demonstrate that paracrine retinoid signaling is essential between E7.5-E9.5 for NCC entry into the gut. Vagal NCC form and migrate in Rdh10 mutant embryos but fail to enter the foregut. Comparative RNA-sequencing revealed Ret-Gdnf-Gfra1-signaling which is critical for vagal NCC chemotaxis is downregulated in Rdh10 mutants and furthermore that the composition of the extracellular matrix through which NCC migrate is altered, particularly by increased collagen deposition. Collectively this restricts NCC entry into the gut, demonstrating that Rdh10-mediated vitamin A metabolism and RA signaling pleiotropically regulates the NCC microenvironment during ENS formation and in the pathogenesis of HSCR.

2022-02-01 | GSE166625 | GEO

Transcriptomic Profiling of Vagal and Sacral Level Neural Crest Cell from Mouse Embryos Using Next Generation Sequencing

Project description:The ENS of vertebrates develops from neural crest cell (NCC) deriving from mainly the vagal neural crest, while NCCs from the sacral level to a less extent. In mouse embryos, the vagal NCCs emigrate from the neural tube adjacent to the somite level from 1-7 at Embryonic day (E)9.0, and sacral NCCs emigrate from the neural tube adjacent to the level of somites caudal to somite 24 in the mouse (in the chick, caudal to somite 28) at E9.5. The spatial difference in cell colonization between vagal and sacral NCCs is that vagal NCCs completely colonize the whole gut, while the distribution of sacral NCCs is only restricted to the hindgut segment. To determine the differences between these two groups of cells, we isolated vagal and sacral NCCs by neural tube explant culture and then performed high-throughput RNA-seq to examine the transcriptional variation. We analyzed that differentially expressed genes (DEGs) by gene ontology (GO) analysis in which the DEGs were enriched in cell adherin, proliferation, transcriptional regulation, et al. This study might help to explore the underlying basis for the different cell behaviors between vagal and sacral NCCs during mouse embryonic development.

2021-06-25 | GSE178834 | GEO

Next Generation Sequencing Analysis of miRNA expression profile in E9.5 mouse embryonic heart

Project description:Purpose: To identify miRNA expresssion profiles in E9.5 mouse embryonic heart Methods: Total RNA of E9.5 heart were extracted with TRIZOL, miRNA deep sequencing were performed in using Illumina Hiseq 2500, SE50 (RIBOBIO, http://www.ribobio.com/), producing over 10 million reads from each sample. Clean reads were mapped to mouse genome (mm9), using miRDeep2 Results: MiRNAs that were highly expressed in E9.5 embryonic heart were identified Conclusions: Results provide insight into the role of miRNAs function in E9.5 embryonic heart development

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Single cell RNA-seq analysis of CNCCs at embryonic E9.5

Project description:Single cell RNA-seq analysis of CNCCs at embryonic E9.5

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Next Generation Sequencing Analysis of gene expression profile in E9.5 Mesp1Cre/+/Dgcr8-/- embryonic heart cells transfected with NC miRNA and miR-541 mimics

Project description:Purpose: To compare the E9.5 Dgcr8 conditional knockout embryonic heart cells transfected with NC miRNA and miR-541 mimics Methods: In vitro cultured E9.5 Dgcr8 conditional KO heart cells transfected with miR-541-5p and NC miRNA were extracted with TRIZOL 48hrs after transfection, and 10ng total RNA was reverse transcribed and amplified by Smart-seq2 protocol as described (Picelli et al., 2014). Duplicated biological samples were analyzed using Illumina HiSeqX10, Clean reads were mapped to mouse genome (mm9) using BWA software. Results: Genes differentially expressed in E9.5 Dgcr8 cKO embryonic heart cells transfected with NC miRNA and miR-541 were identified. Conclusions: miRNA-541 significantly changes the gene expression profiles of E9.5 Dgcr8 cKO embryonic heart cells and promote the cardiac function

2018-09-12 | GSE96647 | GEO

RNAseq analysis on e9.5 mutant mouse hearts

Project description:We report RNAseq analysis on RNA from e9.5 hearts of Asb2 mutant and Asb2.Flna double mutants with controls. The goal of this study is to identify Asb2 downstream targets in the heart as well as targets that are corrected in the Asb2.Flna double mutant vs the Asb2 singe mutants.

2020-02-19 | GSE145495 | GEO

HDAC1 binding regions in mouse embryonic limbs

Project description:HDAC1 binding regions in mouse embryonic limbs

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Global gene expression changes in E9.5 cardiopharyngeal mesoderm (CPM) of Chd7 mutants versus controls

Project description:Global gene expression changes in E9.5 cardiopharyngeal mesoderm (CPM) of Chd7 mutants versus controls

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GLI3 binding regions in mouse embryonic forelimb buds

Project description:GLI3 binding regions in mouse embryonic forelimb buds

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Genome-nuclear lamina interactions in the heart at embryonic days E9.5 and E12.5

Project description:Lamin B1 ChIP-seq analysis of microdissected whole hearts from E9.5 and E12.5 CD1 embryos. Results provide insight into in vivo genome-nuclear lamina interactions over the course of embryonic development. Progenitor cells require coordinated expression of lineage-specific genes to regulate differentiation into daughter cell types. Epigenetic regulators are ideally positioned to synchronize transcription of disparate genomic loci. Using cardiac development to model progenitor cell behavior, we map genome- lamina interactions in vivo to reveal dynamic changes during cardiac development and propose that Hdac3 mediates chromatin organization and gene positioning in cardiac progenitors to regulate fate decisions.

2018-12-01 | GSE64148 | GEO

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