Chia-Lo / TCR-signal-strength-modulates-antigen-specific-CD8-T-cell-pathogenicity-in-non-obese-diabetic-mice

Thymic Self-recognition-mediated TCR Signal Strength Modulates Antigen-specific CD8+ T Cell Pathogenicity in Non-obese Diabetic Mice

This repository contains the code used in the TCR repertoire R Studio project for drawing the following figures:

• Fig. 7B-E: Comparison of the TRAV gene segment usage (B), TRAJ gene segment usage (C), TRBV gene segment usage (D), and TRBJ gene segment usage (E) within TRA variable and TRB variable genes between CD5hiCD8+ and CD5loCD8+ cells

• Fig. 7F: CDR3α or CDR3β length in amino acids

• Fig. 7G: CDR3 overlapped count matrix

• Fig. 7I: Average hydrophobicity score of CDR3α and CDR3β

• Fig. 7J: Diversity of CDR3α and CDR3β

• Supplemental Figure 6: Pairing VJ gene segments usage in CD5hiCD8+ and CD5loCD8+ cells

Usage

To reproduce the figures, follow these steps:

1. Clone this repository to your local machine.
2. Navigate to the appropriate directory.
3. Open the TCR repertoire R Studio project file.
4. Open the TCR signal strength modulates antigen-specific CD8+ T cell pathogenicity in non-obese diabetic mice.R file.
5. Run the R scripts associated with each figure to generate the plots.

Citation

If you use this code in your research, please cite our paper [Thymic self-recognition-mediated TCR signal strength modulates antigen-specific CD8+ T cell pathogenicity in non-obese diabetic mice].

Contact

For any questions or inquiries, feel free to contact [Chia-Lo Ho] at [[e-mail]].