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.

本数据集为Pogorelyy、Kirk等人2024年发表手稿中经过预处理的T细胞受体（TCR, T-cell receptor）克隆型数据，详细信息请参阅对应代码仓库。

数据集1至4为TIRTL-seq数据，数据集5为10x Genomics单细胞TCR-seq（scTCR-seq）数据，数据集6为带有唯一分子标识符（UMI, Unique Molecular Identifier）的5'RACE TCR-seq数据。

1) exp1_clones.tar.gz
该压缩包包含六个经压缩的文件夹（exp1_plate1至exp1_plate6），其中存储的TCR克隆型数据对应用于生成图2a、e和f的六块384孔板。其中exp1_plate1_clones.tar.gz专用于生成图2b、c和e。

2) manual_TIRTLseq_clones.tar.gz
该压缩包包含来自手动操作TIRTL-seq实验方案的96孔板TCR克隆型数据。实验中使用12通道移液器从384孔主板手动移取PCR2的UDI引物，从A1位置开始跳过交替的行与列。因此，文件名中的孔位与双索引对应原始384孔板的交替行（A、C、…、O）与列（1、3、5、…、23）。

3) aph17pre_exp_clones.tar.gz 与 aph17post_exp_clones.tar.gz
这两个压缩包分别包含抗原非依赖型T细胞扩增实验前后的TCR克隆型数据，对应图2d所用的数据。

4) exp3_clones.tar.gz
该压缩包包含三个文件夹，存储的TCR克隆型数据对应SJTRC供体样本感染严重急性呼吸综合征冠状病毒2（SARS-CoV-2）后的基线（tp1）、急性期（tp2）与恢复期（tp3）三个时间点，用于生成图3与补充材料图1。对于每个时间点，孔位A1-P12（384孔板左半区）对应使用Dynabeads CD8阳性分选试剂盒（Thermo Fisher，赛默飞世尔科技）富集的CD8+ T细胞，而孔位A13-P24（板右半区）对应使用Dynabeads CD4阳性分选试剂盒（Thermo Fisher，赛默飞世尔科技）富集的CD4+ T细胞。

5) 10x_scTCR_seq.tar.gz
本数据集包含10x Genomics Chromium GEM-X单细胞TCR-seq实验的结果。

6) exp3_bulkTCRseq.tar.gz
该数据集为带有UMI计数的5'RACE单链TCRα与TCRβ测序结果（格式为VDJtools标准格式）。其中F1与F2代表生物学重复样本，tp1、tp2与tp3分别代表三个时间点。