Distinct T Cell Receptor (TCR) gene segment usage and MHC-restriction between foetal and adult thymus

This dataset is published in Rowell J et al, eLife 2024 (10.7554/eLife.93493.3).Here we bulk TCR sequenced rearranged TCRbeta and TCRalpha chain sequences in CD3-/lo double positive (DP) (CD4+CD8+CD3-/lo, adult), CD69-DP (CD4+CD8+CD69-, foetus), CD69+DP (CD4+CD8+CD69+, foetus), CD3+/hi DP (CD4+CD8+CD3+/hi, adult), CD4+CD8- single positive (SP4, foetus and adult) and CD4-CD8+ (SP8, foetus and adult) thymocyte populations from the C57/BL6 foetus (E18.5) and young adult (4 weeks) mouse. To examine the influence of the rate of differentiation on variable and joining gene usage, we synchronized the differentiation of adult DP thymocytes by treating young adult mice (4 weeks) with hydrocortisone (HC) to deplete the adult thymus of all but the most mature cells. At 6 days after treatment, we FACS-sorted and TCR sequenced the replenished CD3-/loDP (CD3-/loCD4+CD8+), and CD3+/hiDP (CD3+/hiCD4+CD8+) populations.The TCR libraries were sequenced on an Illumina NextSeq using the NextSeq 500/550 Mid Output Kit v2.5 (300 Cycles). The NextSeq outputs files in the format named binary based call (.bcl) which were converted into FASTQ files using bcl2fastq for downstream processing and then demultiplexed using a pipeline of scripts described previously (Oakes et al., 2017 , Thomas et al., 2013 ): <i>Decombinator_v3.1</i> (available at: <i>https:// github.com/innate2adaptive/Decombinator/</i> ) in Python 2.7.<br>

本数据集发表于Rowell J等人于eLife 2024年发表的研究（DOI: 10.7554/eLife.93493.3）。本研究针对C57/BL6胎鼠（E18.5）及4周龄年轻成年小鼠的多群胸腺细胞开展批量T细胞受体（TCR）测序，获取重排的TCRβ链与TCRα链序列，涉及的细胞群体包括：CD3-/低表达双阳性（DP，CD4+CD8+CD3-/lo，成年鼠）、CD69-DP（CD4+CD8+CD69-，胎鼠）、CD69+DP（CD4+CD8+CD69+，胎鼠）、CD3+/高表达DP（CD4+CD8+CD3+/hi，成年鼠）、CD4+CD8-单阳性（SP4，胎鼠与成年鼠）以及CD4-CD8+单阳性（SP8，胎鼠与成年鼠）。
为探究分化速率对可变基因与连接基因使用偏好的影响，我们通过氢化可的松（HC）处理4周龄成年小鼠，清除成年胸腺中除最成熟细胞外的所有细胞，以此同步化成年DP胸腺细胞的分化进程。处理后第6天，我们通过荧光激活细胞分选（FACS）分选得到经补充的CD3-/loDP（CD3-/loCD4+CD8+）与CD3+/hiDP（CD3+/hiCD4+CD8+）细胞群，并进行TCR测序。
TCR文库采用Illumina NextSeq平台，搭配NextSeq 500/550 Mid Output Kit v2.5（300个循环）进行测序。测序产出的原始文件为二进制碱基调用格式（.bcl），我们通过bcl2fastq工具将其转换为FASTQ文件以用于后续分析，随后使用此前报道的脚本流程进行解复用（Oakes等，2017；Thomas等，2013），具体工具为Python 2.7环境下的<Decombinator_v3.1>（获取地址：<https://github.com/innate2adaptive/Decombinator/>）。