Wu, Fengli
Wu, Yingjie
Yao, Yuanning
Xu, Yuanyuan
Peng, Qi
Ma, Long
Li, Jun
Yao, Xinsheng
Funding for this research was provided by:
National Natural Science Foundation of China (82160279)
Guizhou Provincial High-level Innovative Talents Project (No. (2018) 5637)
Article History
Received: 20 December 2023
Accepted: 17 July 2024
First Online: 19 July 2024
Declarations
:
: All the experimental procedures were carried out entirely under animal welfare guidelines. The collection of bats, mice, buffaloes, and cattle in our laboratory was approved by the Ethics Committee of Zunyi Medical University (the bats and mice project was approved under permit number (2018)2-261, and the buffaloes and cattle project was approved under permit number ZMU21-2203-111). We declare that this study is reported in accordance with the ARRIVE guidelines (). In addition to our own data collection, we also utilized publicly available data from shared databases, such as EMBL-EBI, NCBI, and IMGT, for information on humans (, ), rhesus monkeys (, ) and mice ().
: Not applicable.
: The authors declare no competing interests.
: All the experimental procedures were carried out entirely under animal welfare guidelines. The collection of <i>Mus musculus</i>, <i>Artiodactyla</i> and <i>Chiroptera</i> samples conducted in our laboratory was approved by the Ethics Committee of Zunyi Medical University (the <i>Chiroptera</i> and <i>Mus musculus</i>, project was approved under permit number (2018)2-261, and the <i>Artiodactyla</i> project was approved under permit number ZMU21-2203-111). We declared that this study was reported in accordance with the ARRIVE guidelines (). In addition to our own data collection, we also utilized publicly available data from shared databases, such as EMBL-EBI, NCBI, and IMGT, for information regarding humans (, ), rhesus monkeys (, = PRJ NA74626) and mice ().
: We declared that this study was reported in accordance with the ARRIVE guidelines (). (1) Research design: Our research subjects were <i>Primates</i> (<i>H. sapiens</i> and <i>M. mulatta</i>), <i>Rodentia</i> (<i>M. musculus</i>), <i>Artiodactyla</i> (<i>B. taurus</i> and <i>B. bubalis</i>), and <i>Chiroptera</i> (<i>R. affinis</i> and <i>Hipposideros armiger</i>). (2) The sample sizes were as follows: 13 <i>H. sapiens</i> (human), 6 <i>M. mulatta</i> (rhesus monkey), 6 <i>M. musculus</i> (BALB/c, C57BL/6, and Kunming mice) samples, 18 <i>R. affinis</i> and <i>H. armige</i> samples, and 13 <i>B. taurus</i> (bovine) and <i>B. bubalis</i> (buffalo) samples. Our study did not include a control group, and we compared each group of animals. (3) Randomization: We used a random method to include the study animals. (4) Experimental animals and procedure: Four human thymus samples and four peripheral blood samples were collected from infants aged 7, 52, 107, and 156 days. DNA was extracted from thymus tissues and peripheral blood mononuclear cells (PBMCs), and the TCRβ CDR3 repertoire was constructed using multiplex PCR. Sequencing was conducted on the Illumina platform, and the relevant sample information was obtained from the article (DOI: ). The other five peripheral blood samples were obtained from five healthy donors aged 39, 71, 55, 68, and 41 years. PBMCs were isolated using density gradient centrifugation, and single-cell sequencing was performed on the Illumina HiSeq 3000 platform. The basic information of the samples is available in the published article (DOI:). The mouse samples from our group were collected from 3 female BALB/c mice aged 2 months and 3 Kunming mice. Total RNA was extracted from each sample, and the 5’RACE method was used to construct the TCRβ CDR3 repertoire. Sequencing was performed using an Illumina NovaSeq 6000 platform. In another mouse sample from 3 C57BL/6 tumor-bearing mice aged 6–8 weeks, immunomagnetic bead negative selection was used to pre-enrich total T cells. Single-cell sequencing was performed on the Illumina HiSeq 4000 platform. The basic sample information is derived from a published article (DOI:). One spleen sample and two PBMC samples from a rhesus monkey were used. FACS was employed to stimulate nonproliferating T cells (SRR15249814) and proliferating T cells (SRR15249812). The 5’RACE method was used for the construction of the TCRβ CDR3 repertoire. Single-cell sequencing was performed on the Illumina NextSeq 500 platform. The basic information of the samples was obtained from a published article (DOI: ). One blood sample was obtained from a 5-year-old healthy female Chinese rhesus monkey. PBMCs were isolated using density gradient centrifugation, and total RNA was then extracted. The TCRβ CDR3 repertoire was constructed using 5’RACE, and sequencing was conducted using the Illumina HiSeq 2000 platform. The basic information of the sample can be found in a previously published article (DOI:). The <i>Chiroptera</i> samples were collected from 3 <i>R. affinis</i> and 3 <i>H. armiger</i> in Guizhou, China. Spleen tissue samples were obtained, and total RNA was extracted. The 5’RACE method was employed to construct the TCRβ CDR3 repertoires, and sequencing was performed using the Illumina HiSeq 1500 platform. <i>Artiodactyla</i> samples were collected from 6 buffaloes and 7 bovines, and DNA was extracted from spleen samples. Multiplex PCR was used to construct the TCRβ CDR3 repertoires, and sequencing was performed using the MGISEQ-2000RS platform. (5) Results: All the sequencing data were used for the analysis of the TCRβ CDR3 repertoire. (6) Statistical methods: SPSS (version 29.0) was used for statistical analysis, and we performed statistical analysis using the Mann-Whitney U test. All statistically significant differences are indicated as *<i>P</i> value < 0.05, **<i>P</i> value < 0.01, and ***<i>P</i> value < 0.001.