E-MTAB-7658
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-7658 | ExpressionAtlas | 2019-09-09
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-7658-analysis-methods.tsv | Tabular | |||
| E-MTAB-7658-analytics.tsv | Tabular | |||
| E-MTAB-7658-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-7658-configuration.xml | Xml | |||
| E-MTAB-7658-g2_g1-mvaPlot.png | Other |
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Project description:We adopted an omics (transcriptome, proteome, and metabolome) approach to characterize the lens fiber cells extracted from control (CT) and cigarette smoke (CS) exposed mouse (C57BL/6) eyes. The eight pregnant female mice (gestation days 19-20) were placed in a whole-body exposure smoking chamber and served as a CS-exposed group. The mothers and newborn pups were exposed to CS for five hours/day, five days/week for 110 days. In parallel, age-matched mice were kept in normal cages and served as a control group. The ophthalmic examination revealed no sign of cataracts in CS-exposed and aged-matched CT mice. The ocular lenses were extracted and fiber cells (FC) were separated from the lens epithelium under a microscope. The CT and CS fiber cells were maintained in four biological replicates each consisting of a pool of lens fiber cells from four eyes. The eight biological replicates including four CT and four CS-exposed fiber cells were used for the next-generation-based transcriptome (RNA-Seq), mass-spectrometry-based proteome, and metabolome profiling. RNA-Seq analysis identified the expression (≥1.0 FPKM) of 9,590 and 9,531 genes in CT and CS-exposed fiber cells, respectively. The analysis identified 348 differentially expressed genes, including 186 downregulated and 162 upregulated genes in CS-exposed fiber cells. Proteome profiling revealed a total of 2,424 proteins in CT and CS exposed fiber cells. The analysis identified 42 downregulated and 59 upregulated proteins in CS exposed fiber cells. Metabolome profiling identified a total of 280 metabolites, marked with decreased levels of branched-chain amino acids (BCAAs)-related metabolites in CS exposed fiber cells. In conclusion, we have established a comprehensive omics profile of fiber cells from CS-exposed mice. To the best of our knowledge, this is the first report investigating a comprehensive omics profile of fiber cells from CS-exposed mice.
2022-02-15 | PXD017414 | Pride
Project description:We adopted an omics (transcriptome, proteome, and metabolome) approach to characterize the lens fiber cells extracted from control (CT) and cigarette smoke (CS) exposed mouse (C57BL/6) eyes. The eight pregnant female mice (gestation days 19-20) were placed in a whole-body exposure smoking chamber and served as a CS-exposed group. The mothers and newborn pups were exposed to CS for five hours/day, five days/week for 110 days. In parallel, age-matched mice were kept in normal cages and served as a control group. The ophthalmic examination revealed no sign of cataracts in CS-exposed and aged-matched CT mice. The ocular lenses were extracted and fiber cells (FC) were separated from the lens epithelium under a microscope. The CT and CS fiber cells were maintained in four biological replicates each consisting of a pool of lens fiber cells from four eyes. The eight biological replicates including four CT and four CS-exposed fiber cells were used for the next-generation-based transcriptome (RNA-Seq), mass-spectrometry-based proteome, and metabolome profiling. RNA-Seq analysis identified the expression (≥1.0 FPKM) of 9,590 and 9,531 genes in CT and CS-exposed fiber cells, respectively. The analysis identified 348 differentially expressed genes, including 186 downregulated and 162 upregulated genes in CS-exposed fiber cells. Proteome profiling revealed a total of 2,424 proteins in CT and CS exposed fiber cells. The analysis identified 42 downregulated and 59 upregulated proteins in CS exposed fiber cells. Metabolome profiling identified a total of 280 metabolites, marked with decreased levels of branched-chain amino acids (BCAAs)-related metabolites in CS exposed fiber cells. In conclusion, we have established a comprehensive omics profile of fiber cells from CS-exposed mice. To the best of our knowledge, this is the first report investigating a comprehensive omics profile of fiber cells from CS-exposed mice.
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Project description:Alveolar and tissue macrophages were sorted from Schistosoma-exposed and unexposed mice. The mice were C57Bl6/J background. Schistosoma mansoni exposure was intraperitoneal sensitization and intravenous challenge with purified eggs (see Kumar et al. Am J Respir Crit Care Med. 2015;192(8):998-1008. doi: 10.1164/rccm.201410-1820OC. PMID: 26192556). Samples were pooled from N=5 animals per group. Cell sorting was performed on day 3 after IV challenge. Alveolar macrophages were identified as CD45+F4/80+CD11c+SiglecF+. Tissue macrophages were identified as CD45+F4/80+CD11b+SSClow. The RNA library was prepared using a Kappa Stranded mRNA-Seq kit. RNA sequencing was performed on an Ion Proton platform. Expression analysis was performed using Tophat-Bowtie-Cufflinks with Galaxy online.
2016-07-21 | E-GEOD-84651 | biostudies-arrayexpress
Project description:High-throughput sequencing of life stages and tissues of the flatworm Schistosoma mansoni to be used for further gene editing, gene finding and transcriptome analysis ArrayExpress Release Date: 2010-12-09 Person Roles: investigator Person Last Name: Protasio Person First Name: Anna Person Mid Initials: V. Person Email: ap6@sanger.ac.uk Person Phone: Person Address: Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, Uk Person Affiliation: Wellcome Trust Sanger Institute Person Roles: submitter Person Last Name: Service Person First Name: Submission Person Mid Initials: Person Email: datahose@sanger.ac.uk Person Phone: Person Address: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom Person Affiliation: Wellcome Trust Sanger Institute
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