Transcriptomic profiling of the developing rabbit's lung
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ABSTRACT:
PROVIDER: PRJNA911745 | ENA |
REPOSITORIES: ENA
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Project description:We decompose the genome-wide expression patterns in 38 embryonic human lung (53-154 days post conception/dpc) into their independent, dominant directions of transcriptomic sample variation in order togain global insight of the developing human lung transcriptome.The characteristic genes and their corresponding bioâontologic attribute profile for the latter were identified. We noted the overârepresentation of lung specific attributes (e.g., surfactant proteins) traditionally associated with later developmental stages, and highly ranked attributes (e.g., chemokineâimmunologic processes) not previously reported nor immediately apparent in an early lung development context. We defined the 3,223âgene union of the characteristic genes of the 3 most dominant sources of variation as the developing lung characteristic subâtranscriptome (DLCS). It may be regarded as the minimal gene set describing the essential biology of this process. The developing lung series in this transcriptomic variation perspectiveform a contiguous trajectory with critical time points that both correlate with the 2 traditional morphologic stages overlapping -154 dpc and suggest the existence of 2 novel phases within the pseudoglandular stage. To demonstrate that this characterization is robust, we showed that the model could be used to estimate the gestational age of independent human lung tissue samples with a median absolute error of 5 days, based on the DLCS of their lung profile alone. Repeating this procedure on the homologous transcriptome profiles of developing mouse lung 14â19 dpc, we were able to recover their correct developmental chronology. Whole human fetal lung gene expression profiling from estimated gestational ages 53 to 154 days post conception. Experiment Overall Design: Time series with biological replicates.
2009-09-26 | E-GEOD-14334 | biostudies-arrayexpress
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Project description:Preterm infants are delivered during vulnerable stages of lung development at late canalicular, saccular, or early alveolar phases according to their degree of prematurity. Consequently, they often require medical interventions, especially to support their respiratory system. Preterm birth and post-natal oxygen and mechanical ventilation support can alter programmed patterns of fetal lung development, leading to the instauration of chronic lung diseases. The most significant pulmonary complication of preterm birth is bronchopulmonary dysplasia (BPD). The aim of this study is to delve into the translational power of rabbits as a suitable model of neonatal chronic lung diseases, characterizing the physiological rabbit lung development through the application of histological, transcriptomic, and proteomic analyses on perinatal rabbit lung samples, investigating the impact of preterm birth and its relevance on BPD modeling.
2023-07-04 | GSE220843 | GEO
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Project description:We decompose the genome-wide expression patterns in 38 embryonic human lung (53-154 days post conception/dpc) into their independent, dominant directions of transcriptomic sample variation in order togain global insight of the developing human lung transcriptome.The characteristic genes and their corresponding bio–ontologic attribute profile for the latter were identified. We noted the over–representation of lung specific attributes (e.g., surfactant proteins) traditionally associated with later developmental stages, and highly ranked attributes (e.g., chemokine–immunologic processes) not previously reported nor immediately apparent in an early lung development context. We defined the 3,223–gene union of the characteristic genes of the 3 most dominant sources of variation as the developing lung characteristic sub–transcriptome (DLCS). It may be regarded as the minimal gene set describing the essential biology of this process. The developing lung series in this transcriptomic variation perspectiveform a contiguous trajectory with critical time points that both correlate with the 2 traditional morphologic stages overlapping -154 dpc and suggest the existence of 2 novel phases within the pseudoglandular stage. To demonstrate that this characterization is robust, we showed that the model could be used to estimate the gestational age of independent human lung tissue samples with a median absolute error of 5 days, based on the DLCS of their lung profile alone. Repeating this procedure on the homologous transcriptome profiles of developing mouse lung 14–19 dpc, we were able to recover their correct developmental chronology. Whole human fetal lung gene expression profiling from estimated gestational ages 53 to 154 days post conception. Keywords: Whole lung gene expression profiling, lung development, human fetus.
2009-09-10 | GSE14334 | GEO
Project description:Transcriptomic profiling of M. tuberculosis from human lung tissue
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Project description:Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution
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Project description:Mammalian lung development is a complex morphogenetic process, which initiates near mid-gestation and continues through early postnatal life. The lung arises as two lateral buds that emerge from the ventral foregut endoderm at ~ 9 days after fertilization (in mouse) and undergo numerous rounds of dichotomous branching to form the bronchial tree. This stage of development is referred to as the pseudoglandular phase, histologically characterized by loose mesenchyme surrounding undifferentiated epithelial tubes. We have undertaken a comprehensive gene expression profiling of the entire process of murine lung development using oligonucleotide-based microarrays. Our data reveals the expression pattern of ~ 11,000 genes throughout the morphologic stages of lung development. Examination of the data confirms previously known patterns of expression for extracellular matrix genes and provides new information regarding relationships in temporal expression among groups of these genes. Large-scale cluster analysis reveals associations in the expression profile of specific genes with defined developmental processes. Keywords: time course
2008-04-07 | GSE10889 | GEO