TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing

Processed TCR clonotype data for Pogorelyy, Kirk et al. 2024 manuscript. See the repository for details. 

Datasets 1-4 are TIRTL-seq, dataset 5 is 10x Genomics scTCR-seq, and dataset 6 is 5'RACE TCR-seq with UMIs.

1) exp1_clones.tar.gz

This archive contains six zipped folders (exp1_plate1 to exp1_plate6) with TCR clonotype data corresponding to the six 384-well plates used to create Figure 2a, e, and f. The folder exp1_plate1_clones.tar.gz was specifically used for Figure 2b, c, and e.

2) manual_TIRTLseq_clones.tar.gz

This archive includes TCR clonotype data from the manually performed TIRTL-seq protocol for the 96-well plate. PCR2 UDI primers were manually pipetted from the 384 master plate using a 12-channel pipette, skipping alternate rows and columns starting at A1. Thus, the well numbers and dual indices in the filenames correspond to alternating rows (A, C, …, O) and columns (1, 3, 5, …, 23) of the original 384 plate.

3) aph17pre_exp_clones.tar.gz and aph17post_exp_clones.tar.gz

These archives contain TCR clonotype data for pre- and post-antigen-independent T cell expansion experiments, as used in Figure 2d.

4) exp3_clones.tar.gz

This archive includes three folders with TCR clonotype data for baseline (tp1), acute (tp2), and convalescent (tp3) time points following SARS-CoV-2 infection in SJTRC donor samples, used for Figure 3 and SI Figure 1. For each time point, wells A1-P12 (left half of the 384-well plate) correspond to CD8+ cells enriched using the Dynabeads CD8 Positive Isolation Kit (Thermo Fisher), while wells A13-P24 (right half of the plate) correspond to CD4+ cells enriched with the Dynabeads CD4 Positive Isolation Kit (Thermo Fisher).

5) 10x_scTCR_seq.tar.gz

This dataset contains results from the single-cell TCR-seq protocol (10x Genomics Chromium GEM-X).

6) exp3_bulkTCRseq.tar.gz

Results from 5'RACE single-chain TCRα and TCRβ sequencing (VDJtools format, with counts as UMIs). F1 and F2 represent biological replicates, and tp1, tp2, and tp3 denote time points.