Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq
Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-bas...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2018-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2018/7647980 |
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| _version_ | 1832564235416109056 |
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| author | Zehra Omeroğlu Ulu Salih Ulu Soner Dogan Bilge Guvenc Tuna Nehir Ozdemir Ozgenturk |
| author_facet | Zehra Omeroğlu Ulu Salih Ulu Soner Dogan Bilge Guvenc Tuna Nehir Ozdemir Ozgenturk |
| author_sort | Zehra Omeroğlu Ulu |
| collection | DOAJ |
| description | Calorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (p<0.05). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus. |
| format | Article |
| id | doaj-art-fb88f77d2c6f439a988b23c9edd9ef64 |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2018-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-fb88f77d2c6f439a988b23c9edd9ef642025-02-03T01:11:34ZengWileyInternational Journal of Genomics2314-436X2314-43782018-01-01201810.1155/2018/76479807647980Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seqZehra Omeroğlu Ulu0Salih Ulu1Soner Dogan2Bilge Guvenc Tuna3Nehir Ozdemir Ozgenturk4Faculty of Art and Science, Molecular Biology and Genetics, Yildiz Technical University, Istanbul, TurkeyFaculty of Art and Science, Molecular Biology and Genetics, Yildiz Technical University, Istanbul, TurkeyDepartment of Medical Biology, School of Medicine, Yeditepe University, Istanbul, TurkeyDepartment of Medical Biophysic, School of Medicine, Yeditepe University, Istanbul, TurkeyFaculty of Art and Science, Molecular Biology and Genetics, Yildiz Technical University, Istanbul, TurkeyCalorie restriction (CR), which is a factor that expands lifespan and an important player in immune response, is an effective protective method against cancer development. Thymus, which plays a critical role in the development of the immune system, reacts to nutrition deficiency quickly. RNA-seq-based transcriptome sequencing was performed to thymus tissues of MMTV-TGF-α mice subjected to ad libitum (AL), chronic calorie restriction (CCR), and intermittent calorie restriction (ICR) diets in this study. Three cDNA libraries were sequenced using Illumina HiSeq™ 4000 to produce 100 base pair-end reads. On average, 105 million clean reads were mapped and in total 6091 significantly differentially expressed genes (DEGs) were identified (p<0.05). These DEGs were clustered into Gene Ontology (GO) categories. The expression pattern revealed by RNA-seq was validated by quantitative real-time PCR (qPCR) analysis of four important genes, which are leptin, ghrelin, Igf1, and adinopectin. RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database (GSE95371). We report the use of RNA sequencing to find DEGs that are affected by different feeding regimes in the thymus.http://dx.doi.org/10.1155/2018/7647980 |
| spellingShingle | Zehra Omeroğlu Ulu Salih Ulu Soner Dogan Bilge Guvenc Tuna Nehir Ozdemir Ozgenturk Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq International Journal of Genomics |
| title | Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq |
| title_full | Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq |
| title_fullStr | Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq |
| title_full_unstemmed | Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq |
| title_short | Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq |
| title_sort | transcriptome analysis of the thymus in short term calorie restricted mice using rna seq |
| url | http://dx.doi.org/10.1155/2018/7647980 |
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