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Changes of metabolic genes expression in lungs of bleomycin-treated mice

ABSTRACT: Changes of metabolic genes expression in lungs of bleomycin-treated mice

PROVIDER: PRJNA509902 | ENA |

REPOSITORIES: ENA

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Changes of metabolic genes expression in lungs of bleomycin-treated mice

Project description:Purpose: Explore whether bleomycin treatment will induce changes of metabolic genes expression via next-generation sequencing (NGS) in mouse lung tissues. Methods: Four groups of wild type mice were intratracheally injected with 25 µl PBS or bleomycin (15 mg/kg) after anesthetization. 10 days after bleomycin treatment, lung tissues were removed for RNA collection. Three samples per group were mixed to one sample and used for next RNA purification. RNA samples were then used for high-throughput sequencing according to standard operation based on RNA BGISEQ-500. Results: Using an optimized data analysis workflow, we mapped about 21.9 million sequence reads per sample to the mouse genome (build mm10) and identified 1024 upregulated and 936 downregulated genes in lungs of bleomycin-treated mice. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered metabolic changes of many carbohydrates, amino acid and fatty acid. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in metabolism profiling. Conclusions: Our study represents the first detailed analysis of metabolic changes in lungs of bleomycin-treated mice with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based metabolic genes characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2019-02-19 | GSE123808 | GEO

Lungs from bleomycin-treated 129svJ mice

Project description:Profile of gene expression of lungs from bleomycin-treated C129svJ mice.

2010-06-05 | E-GEOD-452 | biostudies-arrayexpress

Lungs from bleomycin-treated 129svJ mice

Project description:Profile of gene expression of lungs from bleomycin-treated C129svJ mice. Keywords: parallel sample

2003-06-11 | GSE452 | GEO

Lungs from bleomycin-treated A/J mice

Project description:Profile of gene expression of lungs from bleomycin-treated A/J mice.

2010-06-05 | E-GEOD-451 | biostudies-arrayexpress

Lungs from bleomycin-treated A/J mice

Project description:Profile of gene expression of lungs from bleomycin-treated A/J mice. Keywords: parallel sample

2003-06-11 | GSE451 | GEO

mRNA reponse to bleomycin instillation

Project description:Gene expression analysis of C57BL/6 mice challenged by intratracheal bleomycin instillation: mRNA expression profiles were established from lungs following a 14-days PBS or bleomycin administration. One color -experiment with 1 strain of mice (C57BL/6) following a 14-days PBS or bleomycin administration (n=5), corresponding to a total of 10 samples.

2013-02-01 | E-GEOD-34814 | biostudies-arrayexpress

mRNA reponse to bleomycin instillation

2013-02-01 | GSE34814 | GEO

miRNA reponse to bleomycin instillation

Project description:Comparison of C57BL/6 (sensitive) and BALB/c (resistant) mice challenged by intratracheal bleomycin instillation: miRNA expression profiles were established from lungs derived from the two strains, following a 7- or 14-days PBS or bleomycin administration. One color -experiment with 2 strains of mice (C57BL/6 and BALB/c) following a 7- or 14-days PBS or bleomycin administration (n=3), corresponding to a total of 24 samples.

2013-02-01 | E-GEOD-34812 | biostudies-arrayexpress

Drop-seq analysis of bleomycin-treated and control mouse lung single-cell suspensions

Project description:Cell suspensions were prepared from mouse lungs dissociated at baseline or 14 days after intratracheal bleomycin injury, and single cell mRNA-seq libraries were generated with Drop-seq.

2018-10-25 | E-MTAB-7142 | biostudies-arrayexpress

miRNA reponse to bleomycin instillation

2013-02-01 | GSE34812 | GEO

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