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The lncRNA and gene expression profiles during the early stages of mice thymic involution

ABSTRACT: The lncRNA and gene expression profiles during the early stages of mice thymic involution

PROVIDER: PRJNA681222 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13159362_1.fastq.gz	Fastqsanger.gz
	SRR13159362_2.fastq.gz	Fastqsanger.gz
	SRR13159363_1.fastq.gz	Fastqsanger.gz
	SRR13159363_2.fastq.gz	Fastqsanger.gz
	SRR13159364_1.fastq.gz	Fastqsanger.gz

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The lncRNA and gene expression profiles during the early stages of mice thymic involution

Project description:In this study, we collected mice thymus at the age of 1 month, 3 months, and 6 months for sequencing to observe the lncRNA and gene expression profiles in the early stage of thymic involution. RNA-sequencing showed that 340 and 152 differentially expressed genes (DEGs) overlapped at 3- and 6-month-old groups compared with 1-month-old group in males and females, respectively. GO analysis showed that DEGs were significantly enriched in immune response activation, cell proliferation, and fatty acid metabolic process, etc. Next, we identified 15 causal transcription factors. Meanwhile, we identified 16 key DEGs and 29 differentially expressed lncRNAs (DEL), which overlapped both in the male and female groups of 3 months and 6 months for further analysis. Finally, we identified a novel lncRNA–miRNA–mRNA network related to adipocyte deposition using Cytoscape. In summary, this study systematically identified and analyzed the expression profiles of lncRNAs and genes during the early stages of thymic involution, which provided valuable data reference for further exploring the roles of lncRNAs in thymic involution.

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Dynamics of the thymic transcriptome at stages of acute thymic involution in Japanese Black calves with a poor prognosis.

Project description:Transcriptome analysis was performed on the thymus of necropsied Japanese Black calves with a poor prognosis, to clarify the pathology of acute thymic involution, which often happens in farmed calves with a poor prognosis. Gene expression profiles obtained by DNA microarray analysis of eight calf thymuses were grouped into three patterns associated with the histopathological classification of acute thymic involution. Three clusters were arranged by the stage of acute thymic involution based on the first principal component score, suggesting that histopathological conditions have the most significant impact on changes in gene expression profile.

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Project description:The thymus is the site of T lymphocyte development and T cell education to recognize foreign, but not self, antigens. B cells also reside and develop in the thymus, although their function(s) are less clear. During ‘thymic involution,’ a process of lymphoid atrophy and adipose replacement linked to sexual maturation, thymic cells decline. However, thymic B cells decrease far less than T cells, such that B cells comprise ~1% of neonatal thymocytes, but up to ~10% in adulthood in humans. All jawed vertebrates possess a thymus, and we and others have shown that zebrafish (Danio rerio) also have thymic B cells. Here, we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte-specific, fluorophore-labeled transgenic lines, quantifying changes in thymic lymphocytes pre- vs. post-involution. Our results prove that, as in humans, zebrafish thymic B cells increase relative to T cells post-involution. We also performed RNA sequencing (RNA-seq) on D. rerio thymic and marrow lymphocytes of four novel double-transgenic lines, identifying distinct populations of immature T and B cells. Collectively, this is the first comprehensive analysis of zebrafish thymic involution, demonstrating its similarity to human involution, and establishing the highly genetically-manipulatable zebrafish model as a template for involution studies.

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