Table 1. Alignment and quantification statistics in each RNA-seq library sample.

Library	Total reads	Number of reads after trim	Percentage trimmed	Unique alignment reads	Percentage uniquely aligned	Detected all transcripts
E13.5 female PGC lib_1	42729239	42258517	98.9	30889817	73.1	12867
E13.5 female PGC lib_2	42805807	42260667	98.73	30104269	71.2	12354
E13.5 male PGC lib_1	38885293	38523543	99.07	27107722	70.4	13247
E13.5 male PGC lib_2	41244689	40831723	99	28656310	70.2	13104
mESC lib_1	50000000	43082893	86.17	35616704	82.7	13222
mESC lib_2	50000000	43227212	86.45	33783928	78.2	13508