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Comprehensive single cell RNA-seq datasets of mice trachea epithelial progenitors in 6 time points from E12.5 to E18.5 and mature epithelial cells in 2-month mice

ABSTRACT: Comprehensive single cell RNA-seq datasets of mice trachea epithelial progenitors in 6 time points from E12.5 to E18.5 and mature epithelial cells in 2-month mice

PROVIDER: PRJNA640145 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12038134_1.fastq.gz	Fastqsanger.gz
	SRR12038134_2.fastq.gz	Fastqsanger.gz
	SRR12038135_1.fastq.gz	Fastqsanger.gz
	SRR12038135_2.fastq.gz	Fastqsanger.gz
	SRR12038136_1.fastq.gz	Fastqsanger.gz

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Comprehensive single cell RNA-seq datasets of mice trachea epithelial progenitors in 6 time points from E12.5 to E18.5 and mature epithelial cells in 2-month mice

Project description:We delineate the comprehensive developmental trajectories of trachea epithelial progenitors in mice using scRNA-seq datasets. After obtaining the scRNA-seq data in 6 time points from E12.5 to E18.5, we merged all the datasets to describe the establishment process of basal cell population during development, which works as airway facultative stem cells. We found that Krt17 is a novel intermediate marker for basal cell progenitors and Id genes are key transcriptional factors for balancing the proliferation and differentiation programs by promoting their cell cycle.

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Transcriptomic comparison of mouse Epithelial Trachea Cells

Project description:We isolated mouse epithelial trachea cells from FVB mice in order to identify their transcriptomic signature.

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Microarray of Mst1/2 deleted epithelial cells from E18.5 mouse lungs

Project description:ShhCre;Mst1/2flx/flx (Mst1/2 D/D) mice were generated to conditionally delete Mst1 and Mst2 from epithelial progenitors during lung morphogenesis. Lungs from E18.5 control and Mst1/2 D/D mice were mechanically and enzymatically dissociated to generate single cell suspension. Epcam(+) cells were isolated using magnetic microbeads. Microarray analysis of mRNAs isolated from Epcam(+) epithelial cells from E18.5 control and Mst1/2 D/D mice was performed to identify transcriptional changes following deletion of the mammalian Hippo kinases (Mst1 and Mst2) from the embryonic lung. The mammalian Hippo kinases, Mst1 and Mst2, were conditionally deleted in epithelial progenitors of the developing lung using ShhCre. Epcam(+) epithelial cells were isolated from the lungs of E18.5 control and Mst1/2 deleted mice. mRNA isolated from Epcam(+) epithelial cells was analyzed by microarray.

2015-01-01 | E-GEOD-61582 | biostudies-arrayexpress

Microarray of Mst1/2 deleted epithelial cells from E18.5 mouse lungs

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Characterize the unique transcriptional changes in the embryonic trachea of knockout mice

Project description:To further identify the transcriptional changes underlying congenital tracheal malformation in a1H knockout mice, the differential gene expression panel was examined by Affymetrix microarray. To investigate the roles of a1H-regulated genes in tracheal development, we characterize the unique transcriptional changes of early trachea in kockout mice, and compare the expression profiles of knock out trachea with those of wild type trachea. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up or down-regulated genes during this process.

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Transcription profiling of mouse RNA from day E11.5 mouse lung and trachea during MIA overexpression

Project description:In experiments using tissue recombinants and mesenchyme-free culture, we have demonstrated that the entire embryonic respiratory tract epithelium, from the trachea to the distal lung tips, exhibits substantial plasticity in its eventual phenotype that is dependent on the inductive cues it receives from its associated mesenchyme. This observation led us to speculate that the differences between embryonic trachea and lung are defined by limited subset of genes, and that the molecular comparison of these two tissues might provide new information on genes that are important for both lung and trachea development. Microarray experiments designed to identify genes differentially expressed in the E11.5 lung and trachea showed that melanoma inhibitory activity (Mia1) was expressed only in the lung. Mia1 was abundantly expressed during early lung development, but was virtually absent by the end of gestation. Bitransgenic mice expressing MIA under the control of the SFTPC promoter after E16.5, the age when Mia1 is normally silenced, died from respiratory failure at birth with morphologically immature lungs associated with reduced levels of saturated phosphatidylcholine and mature SP-B. Microarray analysis showed significant reductions expression of Sftpa, Sftpb, Abca3, Aqp5, Lzp-s, Scd2, and Aytl2 in lungs misexpressing MIA. Experiment Overall Design: To identify genes differentially expressed in the embryonic lung and trachea, we used microarray analysis to compare RNA from day E11.5 mouse lung and trachea. Experiment Overall Design: To assess the effect of misexpressing MIA on overall lung gene expression, we analyzed RNA from day E18.5 lungs of bitransgenic and control littermates by microarray (Affymetrix MOE430 chip).

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mRNA expression data from whole trachea dissected from either wild-type mice or Scnn1b-Tg mice at post-natal days 0, 3, 10, and 42

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Project description:The larynx, trachea, and esophagus share origin and proximity during embryonic development, with clinical and experimental evidence supporting the existence of neurophysiological, structural, and functional interdependencies before birth. This investigation provides the first comprehensive transcriptional profiling of all three organs during embryonic organogenesis, where differential gene expression gradually assembles the identity and complexity of these proximal organs from a shared origin in the anterior foregut. Through the application of bulk RNA sequencing and gene network analysis of differentially expressed genes (DEGs), both within and across developing embryonic mouse larynx, esophagus, and trachea, we identified co-expressed modules of genes enriched for key biological processes. Organ-specific temporal patterns of gene activity corresponding to gene modules within and across shared tissues during embryonic development (E10.5-E18.5) are described, and the laryngeal transcriptome during vocal fold development and maturation from birth to adult is characterized in the context of laryngeal organogenesis. The findings of this study provide new insights into interrelated gene sets governing organogenesis of this tripartite organ system within the aerodigestive tract, with relevance to multiple families of disorders defined by cardiocraniofacial syndromes.

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