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 ): Decombinator_v3.1 (available at: https:// github.com/innate2adaptive/Decombinator/ ) in Python 2.7.

本数据集由Rowell J等人在eLife 2024年第10卷第7554期（10.7554/eLife.93493.3）发表。本研究对C57/BL6胎鼠（E18.5）和幼年小鼠（4周龄）的胸腺细胞进行大规模TCR测序，获取了CD3-/lo双阳性（DP）（CD4+CD8+CD3-/lo，成年）、CD69-DP（CD4+CD8+CD69-，胎儿）、CD69+DP（CD4+CD8+CD69+，胎儿）、CD3+/hi DP（CD4+CD8+CD3+/hi，成年）、CD4+CD8-单阳性（SP4，胎儿和成年）以及CD4-CD8+（SP8，胎儿和成年）的胸腺细胞群中的TCRbeta和TCRalpha链重排序列。为探究分化速率对可变区和连接区基因使用的影响，通过给予4周龄幼年小鼠（HC，氢化可的松）以同步成年DP胸腺细胞的分化，从而耗竭成熟细胞以外的所有成年胸腺细胞。治疗6天后，我们对补充后的CD3-/loDP（CD3-/loCD4+CD8+）和CD3+/hiDP（CD3+/hiCD4+CD8+）细胞群进行FACS分选和TCR测序。TCR文库采用Illumina NextSeq进行测序，使用NextSeq 500/550 Mid Output Kit v2.5（300循环）进行测序。NextSeq输出文件以二进制调用（.bcl）格式命名，使用bcl2fastq转换成FASTQ文件，之后通过先前描述的脚本管道进行去复用（Oakes et al., 2017，Thomas et al., 2013）。该脚本管道为Decombinator_v3.1（可在https://github.com/innate2adaptive/Decombinator/获取），运行在Python 2.7环境中。