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.