A time course study by mRNA Sequencing to identify transcriptional changes in mice lung development
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE128419 | GEO | 2019/03/19
REPOSITORIES: GEO
Similar Datasets
Project description:Mammalian fetal lung development is a complex biological process.Despite considerable progress, a comprehensive understanding of the dynamic regulatory networks that govern postnatal alveolar lung development is still lacking. The purpose of this study as part of the LungMAP consortium (www.lungmap.net) is to understand the transcriptional changes in the process of mammalian lung development. Method: We isolated endothelial and type II pneumocyte cells from c57BL/6 mice from different time points and performed miRNA array by NanoString technology.
2019-03-25 | GSE128809 | GEO
Project description:The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on several time points. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://www.lungmap.net/
2019-03-29 | GSE129064 | GEO
Project description:Adult mammalian cardiomyocytes (CM) are differentiated post-mitotic cells that lack significant proliferative potential through their inability to reactivate the cell cycle postnatally. In the week after birth, the mammalian heart goes through distinct stages of cell cycle progression and differentiation that govern the development of the mature adult CM phenotype. By establishing the fundamental framework of the molecular signals governing these early events after birth, a potential treatment strategy that restores the heart’s ability to proliferate, and in theory, undergo ‘repair’ after injury could be developed. At 0 days (d), 1d, 3d, 5d, 7d, 10d, and 15d after birth, hearts from C57BL/6J wild-type mice were excised and processed for total RNA isolation. Samples were analyzed by genome-wide messenger RNA (mRNA) microarray profiling. All experiments were performed on age- and sex-matched mice, with equal ratio of male to female mice.
2019-10-01 | E-MTAB-8168 | biostudies-arrayexpress
Project description:The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on postnatal day 1. Distinct populations of epithelial, endothelial, mesenchymal, and immune cells were identified, each containing distinct subpopulations. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://www.lungmap.net/
2019-04-01 | GSE129122 | GEO
Project description:The respiratory system undergoes remarkable structural, biochemical, and functional changes necessary for adaptation to air breathing at birth. To identify dynamic changes in gene expression in the diverse pulmonary cells at birth, we performed Drop-seq based massive parallel single-cell RNA sequencing. An iterative cell type identification strategy was used to unbiasedly identify the heterogeneity of murine pulmonary cell types on postnatal day 1. Distinct populations of epithelial, endothelial, and immune cells were identified, each containing distinct subpopulations. Cell type predictions and signature genes identified using Drop-seq were cross-validated using an independent single cell isolation platform. Temporal changes in RNA expression patterns were compared before and after birth to identify signaling pathways selectively activated in specific pulmonary cell types, demonstrating activation of UPR signaling during perinatal adaptation of the lung. Present data provide the first single cell view of the adaptation to air breathing after birth. All data from the present study are freely accessed at https://www.lungmap.net/
2019-03-29 | GSE128985 | GEO
Project description:Tracing early mammalian lineage decisions by single cell genomics. Lewis Wolpert famously called gastrulation the most important time in your life. During this fascinating process, a pluripotent stem cell population in the early embryo gives rise to the three germ layers from which all organ systems develop. Cell signalling and transcriptional networks are known to regulate aspects of gastrulation, but the precise mechanisms have not been investigated at the single cell level. Thus, new principles remain to be discovered that govern the exit from naïve pluripotency, epigenetic priming, stochasticity in transcriptional programmes, symmetry breaking, and acquisition of heritable transcriptome patterns. We have brought together a consortium of experts in single cell genomics, mammalian postimplantation development, and computational biology to comprehensively tackle this challenge. We will apply recently established single cell genomics techniques for DNA, RNA, and DNA methylation to profile the majority of the cells in mouse postimplantation embryos. This will result in epigenetic and gene expression maps of most cells together with experimentally determined lineage relationships, hence populating a Waddingtonian landscape. Based on such maps, combinations of transcription factors and epigenetic modifiers will be used to experimentally direct differentiation in human iPS cells.
2016-07-08 | E-MTAB-4026 | biostudies-arrayexpress
Project description:A time course study by mRNA Sequencing to identify transcriptional changes in mice lung development
| PRJNA527712 | ENA
Project description:The adult human lung has a very limited capacity to regenerate functional alveoli. In contrast, adult mice have a remarkable capacity for neoalveolarization following either lung resection or injury. The molecular basis for this unique capability to regenerate lung tissue in mice is largely unknown. We examined the transcriptomic responses to single lung pneumonectomy in adult mice in order to elucidate prospective molecular signaling used in this species during lung regeneration. Unilateral left pneumonectomy or sham thoracotomy was performed under general anesthesia (n = 8 mice per group for each of the four time points). Total RNA was isolated from the remaining lung tissue at four time points post-surgery (6 hours, 1 day, 3 days, 7 days) and analyzed using microarray technology. The observed transcriptomic patterns revealed mesenchymal cell signaling, including up-regulation of genes previously associated with activated fibroblasts (Tnfrsf12a, Tnc, Eln, Col3A1), as well as modulation of Igf1-mediated signaling. The data set also revealed early down-regulation of pro-inflammatory cytokine transcripts, up-regulation of genes involved in T cell development and function, but few similarities to transcriptomic patterns observed during embryonic or post-natal lung development. Immunohistochemical analysis suggests that early fibroblast but not myofibroblast proliferation is important during lung regeneration and may explain the preponderance of mesenchymal-associated genes that are over-expressed in this model. This appears to differ from embryonic alveologenesis. These data suggest that modulation of mesenchymal cell signaling and proliferation may act in concert with immunomodulation to control inflammation during post-pneumonectomy lung regeneration in adult mice. Experiment Overall Design: For each of the four time points (6 hr, 1 day, 3 day, 7 day), the mice were divided into two groups: (1) pneumonectomy (PNY) and (2) sham operated (SHAM - thoracotomy without lung resection), with eight animals in each group. One microarray was performed on pooled lung tissue from these 8 animals for each time point. Analysis of expression in PNY vs SHAM animals was performed in two ways: using all four microarrays as replicates in a time-independent analysis, as well as analysis of each time point separately (time-dependent) without replicates.
2009-05-16 | E-GEOD-15999 | biostudies-arrayexpress
Project description:Approximately 60-70% of patients with pulmonary sarcoidosis have a good outcome, with disease that resolves spontaneously. It is unclear why some patients progress to fibrotic disease, and there is currently no marker that differentiates these patients from those with self-limiting lung disease. Using the Affymetrix Human Gene 1.0 ST Array, we examined gene expression in lung tissue samples obtained using bronchoscopic transbronchial biopsy from 8 patients with active but self-limiting pulmonary sarcoidosis and 7 with active, progressive, fibrotic pulmonary disease. Analyses were performed to identify differentially expressed genes between the two groups, and to test for enrichment of sets of genes associated with defined biological processes from the Gene Ontology Consortium, as well as with gene sets derived from published data for idiopathic pulmonary fibrosis (IPF) and hypersensitivity pneumonitis (HP).
2010-01-31 | GSE19976 | GEO
Project description:The aim of this experiment was to use microarray analysis to compare the response of wild type (WT) and C/EBPbeta deficient (KO) mice during a partial hepatectomy time course in hopes of identifying transcriptional targets of C/EBPbeta. In addition, the WT time course alone was examined to analyze mammalian cellular proliferation in vivo. In the partial hepatectomy model, quiescent hepatocytes reenter the cell cycle and progress in a synchronous fashion. This allows for the elucidation of regulatory networks operative in mammalian cell cycle. (Identification of transcriptional networks during liver regeneration (2004) Journal of Biological Chemistry)
2006-10-03 | E-CBIL-16 | biostudies-arrayexpress