Table 2 Selected AIRR-seq datasets. For each of eight datasets we used three samples. Ig: immunoglobulin. GC: germinal center; PB: peripheral blood; SF: synovial fluid; ST: synovial tissue; HC: heavy chain; LC: light chain; sc: single cell
From: Systematic evaluation of B-cell clonal family inference approaches
Dataset | Source | Number of patients, samples | Tissue | Source | Ig chain | Mutation load (%) | Sequencing depth |
|---|---|---|---|---|---|---|---|
D1 | Chronic sialadenitis [40] | 1, 3 | single GC | DNA | HC | 3.1 | 144,626 |
2.5 | 157,020 | ||||||
3.3 | 125,092 | ||||||
D2 | Rheumatoid arthritis [41] | 3,3 | PB | RNA | HC | 2.7 | 88,492 |
1.4 | 52,876 | ||||||
1.3 | 54,075 | ||||||
D3 | Rheumatoid arthritis [41] | 1,3 | ST/SF | RNA | HC | 5.5 | 88,075 |
1.7 | 81,566 | ||||||
1.6 | 109,298 | ||||||
D4 | Healthy donor [42] | 3,3 | PB | scRNA | Paired HC/LC | 1.3 | 962 |
0.2 | 1118 | ||||||
0.4 | 1236 | ||||||
D5 | Healthy donor [43] | 3,3 | PB | scRNA | Paired HC/LC | 3.6 | 452,627 |
4.0 | 540,914 | ||||||
4.1 | 115,728 | ||||||
D6 | HIV infected [44] | 3,3 | PB | RNA | HC | 3.7 | 201,048 |
4.5 | 188,309 | ||||||
5.7 | 239,189 | ||||||
D7 | HIV uninfected [44] | 3,3 | PB | RNA | HC | 3.6 | 147,340 |
5.0 | 155,456 | ||||||
3.2 | 146,121 | ||||||
D8 | Crohn’s disease [36] | 3,3 | PB | RNA | HC | 5.2 | 85,841 |
4.0 | 92,112 | ||||||
4.5 | 131,725 |