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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of rat lung alveolar development

ABSTRACT: Lung alveolarization is a complex process that involves interactions between several cell types and leads to considerable increase in gas-exchange surface area. The step designated secondary septation includes elastogenesis from interstitial fibroblasts. We used microarrays to detail the global programme of fibroblast gene expression that underly secondary septation, and identified numerous genes that undergo signficant changes in expression Experiment Overall Design: Rat lung fibroblats were extemporaneously isolated at successive stages of postnatal development that flank the septation period for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates from three different litters were prepared for each time point.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Jacques Bourbon

PROVIDER: E-GEOD-7491 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling in lung fibroblasts reveals new players in alveolarization.

Boucherat Olivier O Franco-Montoya Marie-Laure ML Thibault Christelle C Incitti Roberto R Chailley-Heu Bernadette B Delacourt Christophe C Bourbon Jacques R JR

Physiological genomics 20071002 1

Little is known about the molecular basis of lung alveolarization. We used a microarray profiling strategy to identify novel genes that may regulate the secondary septation process. Rat lung fibroblasts were extemporaneously isolated on postnatal days 2, 7, and 21, i.e., before, during, and after septation, respectively. Total RNA was extracted, and cRNAs were hybridized to Affymetrix rat genome 230 2.0 microarrays. Expression levels of a selection of genes were confirmed by real-time PCR. In ad ...[more]

PMID: 17911382

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Expression data from rat lung alveolar development

Project description:Lung alveolarization is a complex process that involves interactions between several cell types and leads to considerable increase in gas-exchange surface area. The step designated secondary septation includes elastogenesis from interstitial fibroblasts. We used microarrays to detail the global programme of fibroblast gene expression that underly secondary septation, and identified numerous genes that undergo signficant changes in expression Keywords: Time course

2007-04-12 | GSE7491 | GEO

expression data in lung of mice bearing inducible FGF18 transgene

Project description:Better understanding alveolarization mechanisms could help improving prevention and treatment of diseases characterized by reduced alveolar number, especially bronchopulmonary dysplasia (BPD). Although signaling through fibroblast growth factor (FGF) receptors is essential for alveolarization, involved ligands are unidentified. FGF18 whose expression peaks during alveolar septation is likely to be involved. Herein, a mouse model of inducible, lung-targeted FGF18-transgene was used to advance the onset of FGF18 expression, and genome-wide expression changes were determined. keywords: transgenic mice, alveolarization, angiogenesis, fibrosis, epithelial-mesenchymal transition. Four pairs of simple and double transgenic pups issued from 4 different litters were selected on the basis of FGF18 transgene induction. RNA from the mice lung were extracted and hybridized on Affymetrix microarrays.

2011-07-05 | E-GEOD-22283 | biostudies-arrayexpress

expression data in lung of mice bearing inducible FGF18 transgene

2011-07-06 | GSE22283 | GEO

Expression analysis of genes in Rattus norvegicus lungs at postnatal day 4, 10 and 21 after intrauterine growth restriction induced by low protein diet

Project description:We performed RNA microarray in a low protein diet (LPD) model of IUGR at three key time points of alveolarization process. IUGR and control rat pups had been studied for each time point considered: on postnatal day 4 (P4) before beginning of the alveolarization process, on P10, peak of alveolarization process and on P21 at the end of it. A twelve chip study using total RNA extracted from 14 whole lungs intrauterine growth restricted rat pups compared to 15 controls. RNA was extracted at three key time points of alveolarization in postnatal life. RNA was pooled by groups of 2 ou 3 before analysis.

2014-10-29 | E-GEOD-56956 | biostudies-arrayexpress

Dkk4 and Eda regulate distinctive developmental mechanisms for subtypes of mouse hair-2

Project description:Dkk4 transgenic mice in Tabby background lack hair follicle formation. Gene expression profiling showed significant down regulation of Shh pathway genes at E16.5 and E17.5, the secondary hair follicle induction stages. Keywords: development or differentiation design,genetic modification design To define target genes of Dkk4 during secondary hair follicle induction, we carried out microarray experiments with mouse back skin samples that from 2 developmental time points including E16.5 and E17.5 of Tabby and Tabby background Dkk4 transgenic mice.

2010-09-03 | E-GEOD-19312 | biostudies-arrayexpress

Expression data of influenza A-infected human type I-like alveolar epithelial cells

Project description:Pandemic influenza H1N1 (pdmH1N1) virus causes mild disease in humans but occasionally leads to severe complications and even death, especially in those who are pregnant or have underlying disease. Cytokine responses induced by pdmH1N1 viruses in vitro are comparable to other seasonal influenza viruses, suggesting the cytokine dysregulation as seen in H5N1 infection is not a feature of the pdmH1N1 virus. However, a comprehensive gene expression profile of pdmH1N1 in relevant primary human cells in vitro has not been reported. Type I alveolar epithelial cells are a key target cell in pdmH1N1 pneumonia. We carried out a comprehensive gene expression profiling using the Affymetrix microarray platform to compare the transcriptomes of primary human alveolar type I-like alveolar epithelial cells infected with pdmH1N1 or seasonal H1N1 virus. Primary type II alveolar epithelial cells were isolated from human non-malignant lung tissue of three patients who underwent lung resection, and cells were differentiated to type I-like before use. Type I-like alveolar epithelial cells were mock infected, or infected with pdmH1N1 or seasonal H1N1 viruses at a multiplicity of infection (MOI) of two. Total RNA was extracted from cells after 8h post-infection, and gene expression profiling was performed using an Affymetrix Human Gene 1.0 ST microarray platform.

2010-10-06 | E-GEOD-24533 | biostudies-arrayexpress

Expression data from 6 day-old Atxn1L-/- and Atxn1-/- lung tissues

Project description:Although expansion of a polyglutamine tract in ATAXIN1 (ATXN1) causes Spinocerebellar ataxia type 1, the functions of wild-type ATXN1 and ATAXIN1-Like (ATXN1L) remain poorly understood. To gain insight into the function of these proteins, we generated and characterized Atxn1L-/- and Atxn1-/- ; Atxn1L-/- double mutant animals. We found that Atxn1L -/- mice have several developmental problems including hydrocephalus, omphalocoele and lung alveolarization defects. These phenotypes are more penetrant and severe in Atxn1-/- ; Atxn1L-/- mice, suggesting that Atxn1 and Atxn1L are functionally redundant. To unravel the molecular mechanism underlying the alveolarization defect in Atxn1-/- mice, we carried out microarray analyses using total lung RNA from WT, Atxn1-/- and Atxn1L-/- mice Lung tissues were dissected from 6 day old mice from either Atxn1 heterozyous intercrosses or Atxn1L heterozygous intercrosses. We collected lung tissue samples from 4 pairs of WT and Atxn1-/- amd 3 pairs of WT and Atxn1-/- mice. Total RNA extracted from the samples was subjected to microarray analysis using Affymetrix mouse gene ST 1.0 array. GSM731591-GSM731598 (Atxn1L KO and controls) and GSM731599-GSM731604 (Atxn1 KO and controls) were RMA-processed separately.

2011-11-06 | E-GEOD-29551 | biostudies-arrayexpress

A new identified suppressor of Cdc7p/SepH kinase, PomA, regulates fungal asexual reproduction via affecting phosphorylation of MAPK-HogA

Project description:The septation initiation network (SIN), composed of a conserved SepH (Cdc7p) kinase cascade, plays an essential role in fungal cytokinesis/septation and conidiation for asexual reproduction, while the mitogen-activated protein kinase (MAPK) pathway depends on successive signaling cascade phosphorylation to sense and respond to stress and environmental factors. In this study, a SepH suppressor–PomA in the filamentous fungus A. nidulans was identified as a negative regulator of septation and conidiation such that the pomA mutant was able to cure defects of sepH in septation and conidiation and overexpression of pomA remarkably suppressed septation. Under the normal cultural condition, SepH positively regulates the phosphorylation of MAPK-HogA, while PomA reversely affects this process and the phosphorylated HogA in MAPK could be a downstream product of the activated SIN. However, under the osmostress condition, the induced phosphorylated HogA is capable of bypassing the requirement of SepH to fulfill septation and conidiation. Findings demonstrate that crosstalk exists between the SIN and MAPK pathways.

2019-06-17 | PXD012514 | Pride

Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: A model for “active” disease

Project description:Genomic profiling of RNA from cultured human fibroblasts of donor samples in the 10-14th passage was carried out to determine expression changes in the fibroblasts of individual with different degrees of pulmonary fibrosis. Donors consisted of individuals with rapid progressing pulmonary fibrosis, slow progressing pulmonary fibrosis, or no fibrosis. Genomic characterization of cultured human fibroblasts from donor samples was carried out in samples from donors with from 3 groups: rapid progressing pulmonary fibrosis, slow progressing pulmonary fibrosis, and non-fibrotic individuals. Large RNA (> ~ 200bp) was isolated from fibroblast cultures. Purified total RNA was amplified and labeled using NuGen Ovation kits (NuGEN Technologies, Inc., San Carlos, CA) and RNA from samples was hybridized to Affymetrix HG-U133 plus 2.0 arrays.

2013-04-10 | E-GEOD-44723 | biostudies-arrayexpress

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [BrdU]

Project description:BrdU profiling of replication activity in hydroxyurea treated synchronous culture of fission yeast. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Cdc25-22 cells carrying thymidine kinase and human nucleoside transporter expression modules were arrested at the G2/M boundary. After release into the cell cycle in minimal medium supplemented with hydroxyurea and 5â-bromo-2â-deoxyuridine (BrdU) cells were collected at time corresponding to maximal septation index and fixed by treatment with sodium azide. BrdU labeled DNA was recovered by immunoprecipitation, amplified by random-primed PCR and after conjugation with Cy5 (IP) or Cy3 (input DNA) analyzed on Agilent 60mer array.

2016-06-09 | E-GEOD-78819 | biostudies-arrayexpress

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