Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29511668", "kind": "science-record", "revision": 8, "content_hash": "sha256:9991c0122ed4b3abbb013bdff4873bd45061f35f75a6463b48af4a7ae49bf0e4", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T22:43:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome Analysis of the Thymus in Short-Term Calorie-Restricted Mice Using RNA-seq.", "doi": "10.1155/2018/7647980", "pmid": "29511668", "authors": ["Zehra Omeroğlu Ulu", "Salih Ulu", "Soner Dogan", "Bilge Guvenc Tuna", "Nehir Ozdemir Ozgenturk"], "journal": "International journal of genomics", "year": 2018, "abstract": "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.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) were identified with Cuffdiff, a part of Cufflinks package [51]. The DEGs were filtered employing the false discovery rate (FDR) correction, Fisher's exact test, and a fold-change method, exhibiting a corrected p value not greater than 0.05 (p value < 0.05) along with a fold change value not less than 2.0. All of the data produced by a Cuffdiff analysis was visualized and integrated with R [52].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29511668", "locator": "sections[5] \"2.3. RNA-seq Data Processing\" paragraph 2", "quote": "The differentially expressed genes (DEGs) were identified with Cuffdiff, a part of Cufflinks package [51]. The DEGs were filtered employing the false discovery rate (FDR) correction, Fisher's exact test, and a fold-change method, exhibiting a corrected p value not greater than 0.05 (p value < 0.05) along with a fold change value not less than 2.0. All of the data produced by a Cuffdiff analysis was visualized and integrated with R [52]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-seq data has been deposited in NCBI Gene Expression Omnibus (GEO) database under accession number GSE95371.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29511668", "locator": "sections[4] \"2.2. 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