Table 1.
Data processing metrics for small RNA reads
| Histology | No of samples | Sequences | Aligned | Unique aligned | Assigned to miRNAd | Assigned to small RNA contigs |
|---|---|---|---|---|---|---|
| Normala | 12 | 137,821,767 | 107,214,046 (77.8 %) | 69,211,744 (50.2 %) | 44,584,258 | 361,269,586 |
| Carcinoma in Situ b | 3 | 46,285,700 | 36,839,326 (79.6 %) | 27,608,395 (59.6 %) | 24,977,605 | 55,763,124 |
| Embryonal Carcinoma cell linesc | 6 | 24,651,693 | 14,504,501 (58.8 %) | 12,270,382 (49.8 %) | 4,076,105 | 12,679,068 |
| Embryonal Carcinoma | 5 | 60,049,727 | 45,515,442 (75.8 %) | 22,271,004 (37.1 %) | 14,412,704 | 21,9138,834 |
| Yolk Sac Tumor | 4 | 33,808,192 | 25,482,718 (75.4 %) | 14,831,132 (43.9 %) | 15,221,965 | 80,580,426 |
| Seminoma | 3 | 24,687,396 | 18,385,722 (74.5 %) | 12,754,266 (51.7 %) | 5,327,777 | 52,606,953 |
| Teratoma | 3 | 43,576,658 | 35,638,201 (81.8 %) | 21,503,877 (49.3 %) | 30,109,084 | 76,746,231 |
| Chorio-carcinoma | 1 | 80,68,838 | 6,171,431 (76.5 %) | 4,171,369 (51.7 %) | 4,545,330 | 8,955,051 |
| TOTAL | 37 | 378,949,971 | 289,751,387 (76.5 %) | 184,622,169 (48.7 %) | 143,254,828 | 867,739,273 |
Raw sequence data from the small RNA sequencing dataset. Percentage >100 % is due to multiple hits in the sequence mapping. aThe normal samples are from 11 healthy men and 1 biopsy from histological normal tissue adjacent to a tumor in a TGCT patient. b The cell line samples consists of cells from the embryonal carcinoma lines NT2 and 2102Ep. c Evaluation of cryosections of the carcinoma in situ samples estimated presence of CIS cells in 10 %, 50 %, and 100 % of the seminiferous tubuli. d As annotated by miRBase