Skip to main content

Table 1 Data processing metrics for small RNA reads

From: Profiling of the small RNA populations in human testicular germ cell tumors shows global loss of piRNAs

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
  1. 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