Tph cells share large portions of repertoires with Trh cells. Tph cells in the blood and CD69⁺ or CD69^- Trh subsets in the liver and lung of cGVHD recipients 30 days after HCT were isolated for TCR-Seq analysis to compare the similarity of TCR repertoires. Because of lymphopenia in cGVHD mice, peripheral blood mononuclear cells from 15 mice were pooled for a single sorting experiment and liver or lung mononuclear cells were pooled from 5 mice. (A, C) Scatterplot comparison of TRB and TRA repertoire fractions between Tph cells and liver CD69⁺ or CD69^- Trh cells. (B, D) TCR repertoire similarity of TRB and TRA in A and C was compared by Morisita’s overlap index. (E, G) Scatterplot comparison of TRB and TRA repertoire fractions between Tph cells and lung CD69⁺ or CD69^- Trh cells. (F, H) TCR repertoire similarity of TRB and TRA in E and G was compared by Morisita’s overlap index. (I) Heatmap of gene use of TRB-V segments among Tph from blood, CD69^-, and CD69⁺ Trh subsets from the liver and lung. (J) Two representative TCR clonotypes TCR-Vα2.2-Vβ3 and TCR-Vα2.2-Vβ8.3 were measured by flow cytometry among Tph cells from blood, Trh cells from the liver, and lung of cGVHD recipients.