Online-Only Table 7.
10X Genomics Chromium Genome Sequencing (10X WGS) data sets for fresh DNA extracted from HCC1395BL and HCC1395 cell lines.
| Sample ID | Sample | Biosample | Platform | Machine model | library Protocol (Input amount) | Total Reads | Total Mapped Reads | molecule length mean (Kb) | %mapped reads | mean depth | zero coverage | % pcr duplication | large sv calls | short deletion calls | longest phase block (Mb) | n50 phase block (Mb) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CHR_IL_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,212,061,014 | 2,092,851,168 | 72.00 | 94.61 | 92 | 1.42 | 8.32 | 336 | 4033 | 32 | 0.9 |
| CHR_IL_T_2 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,266,945,480 | 2,147,917,753 | 76.00 | 94.75 | 94 | 1.41 | 7.03 | 338 | 4257 | 31.9 | 0.9 |
| CHR_IL_T_3 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,329,482,706 | 2,226,020,206 | 77.00 | 95.56 | 99 | 1.40 | 6.44 | 330 | 4626 | 26.7 | 0.8 |
| CHR_NC_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,406,971,948 | 1,366,399,528 | 54.00 | 97.12 | 61 | 1.53 | 5.84 | 304 | 4438 | 14.9 | 1.2 |
| CHR_EA_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,321,617,070 | 1,279,515,774 | 67.00 | 96.81 | 57 | 1.40 | 11.87 | 295 | 5267 | 16.9 | 0.6 |
| CHR_FD_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,064,469,438 | 1,015,823,822 | 64.00 | 95.43 | 45 | 1.45 | 5.63 | 266 | 4439 | 17.5 | 0.7 |
| CHR_FD_T_2 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,070,778,002 | 1,027,173,140 | 66.00 | 95.93 | 45 | 1.45 | 4.37 | 265 | 4313 | 15.2 | 0.7 |
| CHR_FD_T_3 | HCC1395 | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,070,863,374 | 1,020,779,776 | 66.00 | 95.32 | 45 | 1.50 | 7.10 | 258 | 4382 | 18.4 | 0.8 |
| CHR_NV_T_1 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,763,309,906 | 2,686,525,126 | 67.60 | 97.22 | 119 | 1.44 | 12.05 | 353 | 3863 | 22.9 | 0.7 |
| CHR_NV_T_2 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,604,341,620 | 2,529,765,476 | 62.77 | 97.14 | 113 | 1.43 | 14.52 | 354 | 3705 | 17.6 | 0.6 |
| CHR_NV_T_3 | HCC1395 | Fresh cells | HiSeq | HiSeq 4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,614,247,622 | 2,546,038,714 | 61.83 | 97.39 | 114 | 1.43 | 13.23 | 350 | 3701 | 20.0 | 0.6 |
| CHR_IL_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,134,749,498 | 2,025,432,377 | 70.00 | 94.88 | 90 | 0.82 | 7.50 | 25 | 3507 | 33.6 | 7.5 |
| CHR_IL_N_2 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,202,527,584 | 2,107,633,315 | 72.00 | 95.69 | 93 | 0.82 | 7.16 | 23 | 3532 | 30.3 | 6.7 |
| CHR_IL_N_3 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,380,468,964 | 2,279,808,496 | 70.00 | 95.77 | 101 | 0.81 | 6.98 | 24 | 3460 | 24.4 | 7 |
| CHR_NC_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 3000/4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,420,063,110 | 1,383,151,777 | 66.00 | 97.40 | 62 | 0.90 | 6.79 | 24 | 3751 | 19.8 | 4.5 |
| CHR_EA_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,204,338,932 | 1,157,467,982 | 67.00 | 96.11 | 52 | 0.87 | 10.70 | 21 | 4717 | 19.3 | 4.4 |
| CHR_FD_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,079,294,448 | 1,047,436,008 | 63.00 | 97.05 | 46 | 0.91 | 5.02 | 24 | 3824 | 27.8 | 3.8 |
| CHR_FD_N_2 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,074,129,460 | 1,037,897,214 | 63.00 | 96.63 | 46 | 0.92 | 4.47 | 20 | 3827 | 18.4 | 3.9 |
| CHR_FD_N_3 | HCC1395BL | Fresh cells | HiSeq | HiSeq X10 | 10X Chromium Genome Library preparation v2 (1250 ng) | 1,069,034,706 | 1,026,145,348 | 61.00 | 95.99 | 45 | 0.79 | 4.65 | 20 | 3994 | 15.7 | 3.3 |
| CHR_NV_N_1 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,745,515,070 | 2,673,917,830 | 61.23 | 97.39 | 119 | 0.83 | 10.72 | 85 | 3063 | 25.4 | 4.7 |
| CHR_NV_N_2 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,610,495,528 | 2,542,805,354 | 55.45 | 97.41 | 114 | 0.83 | 14.18 | 93 | 3165 | 30.0 | 4.2 |
| CHR_NV_N_3 | HCC1395BL | Fresh cells | HiSeq | HiSeq 4000 | 10X Chromium Genome Library preparation v2 (1250 ng) | 2,614,793,942 | 2,538,150,020 | 56.52 | 97.07 | 113 | 0.83 | 12.25 | 93 | 3181 | 30.3 | 4.4 |
Libraries were made from Chromium Genome Library preparation v2 kit and sequenced by five sequencing centers on Illumina HiSeq 3000/4000, HiSeq X10 for cross-site comparision.