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

Table 1 Data processing metrics for small RNA reads

Histology	No of samples	Sequences	Aligned	Unique aligned	Assigned to miRNA^d	Assigned to small RNA contigs
Normal^a	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 lines^c	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

ISSN: 1476-4598