Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1232954 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32622113_1.fastq.gz | Fastqsanger.gz | |||
| SRR32622113_2.fastq.gz | Fastqsanger.gz |
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Project description:Inbreeding leads to a reduction in genetic diversity and an elevated likelihood of expressing recessive defective genes, which adversely affect the development of the immune system and render individuals and populations more susceptible to carcinogenic factors, consequently heightening the risk of cancer. Through investigating the function and extent of immune cell interaction in peripheral blood mononuclear cells (PBMCs) of inbred individuals, one can gain a comprehensive understanding of the impact of inbreeding on various aspects of the immune system, including diversity, self-tolerance, immune responsiveness, susceptibility to diseases, and other related areas. Currently, the wild Amur tiger population in China exhibits a moderate degree of inbreeding, with a probability exceeding 90% that it will be deemed extinct within the forthcoming century. However, the impact of inbreeding on the immune system remains ambiguous, presenting numerous challenges for the development and implementation of conservation strategies. The present study presents, for the first time, a detailed single-cell sequencing atlas of peripheral blood samples obtained from Amur tigers, delineating eight distinct cell types. Research findings show that inbred individuals have a lower percentage of lymphocytes and cDC2 cells, as well as diminished intercellular interactions compared to non-inbred individuals. Meanwhile, inbred individuals exhibited significantly increased expression of signaling pathways such as TGFb, APRIL, BAG, GRN, and VISFATIN, which are closely associated with inflammation and cancer. Moreover, the WGCNA analysis unveiled the core gene regulatory network specific to inbred individuals, highlighting a robust correlation between inbreeding and the cancer-related gene YTHDC2. Our study presents a comprehensive analysis of PBMC characteristics in the Amur tigers and reveals the possibility of increased susceptibility to cancer and inflammation associated with inbreeding. These findings provide novel insights into the immune heterogeneity in the inbred Amur tiger and furnish valuable data supporting timely treatment for affected individuals.
2025-10-30 | E-MTAB-15936 | biostudies-arrayexpress
Project description:Genetic conservation of the Amur tiger (PRJCA037625)
| PRJDB38590 | ENA
Project description:Gene expression and immune cell heterogeneity in inbred Amur tiger
| PRJEB101974 | ENA
Project description:MicroRNA (miRNA) is a class of functional non-coding small RNA with 19-25 nucleotides in length. Amur grape (Vitis amurensis Rupr.) is an important wild fruit crop with the strongest cold resistance in the Vitis genus and is used as an excellent breeding parent for grapevine, and with growing interest in terms of wine production. To date, there is a relatively large number of grapevine miRNAs (vv-miRNAs) from cultivated grapevine varieties such as Vitis vinifera L. and hybrids of V. vinifera and V. labrusca, but there is no report on miRNAs from Vitis amurensis Rupr, a wild grapevine species. In this study, a small RNA library from Amur grapes was constructed and Solexa technology used to perform deep sequencing of the library followed by subsequent bioinformatics analysis to identify new miRNAs. In total, 126 conserved miRNA belonging to 27 miRNA families were identified, and 34 known but non-conserved miRNAs were also found. Significantly, 72 new potential Amur grapevine-specific miRNAs were discovered. The sequences of these new potential va-miRNAs were further validated through miR-RACE, accumulation of 18 new va-miRNAs in seven tissues of grapevines were also confirmed by real time RT-PCR (qRT-PCR) analysis, and expression levels of va-miRNAs in flowers and berries were basically consistent in identity to those from deep sequenced sRNAs libraries of independent corresponding tissues. We also describe the conservation and variation of va-miRNAs using miR-SNPs and miR-LDs during plant evolution based on comparison of orthologous sequences, and revealed the number and sites of miR-SNP of diverse miRNA families exhibited distinct divergence. Finally, 346 target genes for the new miRNAs were predicted and they include a number of Amur grapevine stress tolerance genes and many genes regulating anthocyanin systhesis and sugar metabolism. Deep sequencing of short RNAs from Amur grapes flowers and fruits identified 72 new potential miRNAs and 34 known but non-conserved miRNAs, indicating that specific miRNAs exist in Amur grapes. These results show that a number of regulatory miRNAs exist in Amur grapes and play an important role in Amur grape growth, development, and response to abiotic or biotic stress.
2011-12-16 | GSE34169 | GEO