Cryptic leukemia antigens share homology with microbial epitopes and stimulate T-cell responses in healthy donors

The dataset contains processed T-cell receptor repertoire sequencing data accompanying the manuscript: "Cryptic leukemia antigens share homology with microbial epitopes and stimulate T-cell responses in healthy donors" by Rulleau et al. DOI: https://doi.org/10.64898/2025.12.01.691479 Experimental details: TCR β-chain repertoire profiling. Bulk TCR repertoire profiling was performed from sorted multimer-positive and -negative CD8+ T cell RNA isolated as above using next-generation sequencing (NGS) targeting the hypervariable CDR3 of TCRβ. TCRβ amplicon libraries were prepared from 25 ng total RNA with the Oncomine TCR Beta-SR Assay for RNA (Thermo Fisher Scientific). The TCRβ libraries obtained were quantified on the ViiA 7 real-time PCR system with the Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific). NGS was completed on the Ion S5 semiconductor platform using an Ion 540 chip prepared with the Ion Chef System (all from Thermo Fisher Scientific). TCRβ repertoire analysis was completed using the Ion Reporter software (Thermo Fisher Scientific) and Immunarch package (R software). 5'RACE PCR and alpha/beta TCR chain sequencing. Previously extracted RNA was used to amplify and capture the integrity of the V(D)J variable regions of the α and β chains of TCRs contained in the peptide-specific CD8 T cell repertoire. For this purpose, rapid amplification of complementary DNA ends by polymerase chain reaction (5' RACE PCR) was performed using the SMARTer® Human TCR α/β Profiling Kit v2 (Takara Bio). Amplicons were then purified and size selected using solid phase immobilization beads (NucleoMag beads). Next-generation sequencing was performed at the Institute for Research in Immunology and Cancer (IRIC) using the Illumina Miseq instrument. The Miseq 600-cycle kit was used to cover the integrity of the VDJ regions. Sequences were then pre-processed and analyzed using MIXCR and Immune eProfiler software (Takara Bio). TCR repertoire diversity was analyzed using the Immunarch package, R version 4.1.2 and R studio version 2022.02.1+461. In addition, based on the annotations of the V and J rearrangements and the obtained CDR3 sequence, the complete TCR sequence of the most abundant clonotypes was determined using the Stitchr package.