Table 1 The summary table presents six additional reference datasets from 10X Genomics. Summary statistics regarding FastQ reads, cell barcodes, and UMI barcodes are provided. Cost-benefit analysis is performed for each dataset and the optimal shared design is summarized, with a minimum overall similarity constraint is set to 0.75, along with costs calculated for the optimal shared design and for the original reference dataset respectively, assuming the same unit price
From: A realistic FastQ-based framework FastQDesign for ScRNA-seq study design issues
Brain5k | Heart5k | Jejunum5k | Liver5k | Pbmc5k | Lung5k | |
|---|---|---|---|---|---|---|
Species | Mus musculus | Mus musculus | Homo sapiens | Mus musculus | Homo sapiens | Mus musculus |
Organ | Brain | Heart | Jejunum | Liver | PBMC | Lung |
FastQ Reads | ||||||
Total | 204,596,690 | 190,606,331 | 121,378,620 | 192,920,732 | 182,330,834 | 232,479,932 |
Denoised | 127,761,504 (62.4%) | 145,821,069 (76.5%) | 60,922,906 (50.2%) | 141,114,338 (73.1%) | 164,252,497 (90.1%) | 170,987,117 (73.5%) |
Valid | 68,671,865 (33.6%) | 103,425,786 (54.3%) | 36,532,555 (30.1%) | 102,735,048 (53.3%) | 124,996,459 (68.6%) | 118,145,729 (50.8%) |
Cell Barcode | ||||||
Valid | 7398 | 3281 | 4392 | 6312 | 5131 | 7744 |
Used | 6958 (94.1%) | 3029 (92.3%) | 3407 (77.6%) | 6155 (97.5%) | 4672 (91.1%) | 7315 (94.5%) |
UMI Barcode | ||||||
Valid | 37,855,805 | 18,733,011 | 18,110,700 | 55,354,806 | 48,368,187 | 42,727,410 |
Used | 35,840,609 (94.7%) | 17,596,189 (93.9%) | 9,336,556 (51.6%) | 54,043,335 (97.6%) | 44,277,395 (91.5%) | 35,955,187 (84.2%) |
Optimal Shared Design | ||||||
Valid Cell | 2205 | 3250 | 4350 | 5670 | 1530 | 1540 |
Valid Reads per Valid Cell | 9300 | 9480 | 6640 | 8250 | 17,010 | 10,780 |
Similarity | 75.5% | 76.0% | 76.3% | 75.4% | 75.3% | 75.4% |
Cost (optimal design) | $5,916.44 | $5,851.71 | $6,439.50 | $6,317.62 | $5,569.44 | $5,490.00 |
Original Cost | $8,068.95 | $7,859.09 | $6,820.68 | $7,893.81 | $7,734.96 | $8,487.20 |
