Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine

BMC Genomics

Table 3 Repetitive content in consensus sequences

	Blastocyst embryos			Elongation embryos
Method	Me-RDA	HMe-RDA	HELP cocktail	Me-RDA	HMe-RDA	HELP cocktail
Method	Msp/Hpa	FspBI/BfaI	HELP cocktail	Msp/Hpa	FspBI/BfaI	HELP cocktail
Number of sequences with repetitive content^a	29 777	19 996	27 055	21 490	11 058	26 453
Number of sequences with repetitive content^a	(89.9%)	(68.0%)	(85.6%)	(83.9%)	(44.3%)	(63.3%)
SINE^b	0.6%	9.4%	47.2%	0.3%	6.4%	30.1%
LINE^b	0.3%	30.9%	17.3%	0.1%	10.0%	10.5%
LTR^b	4.6%	8.4%	2.1%	0.4%	5.4%	4.5%
Satellites^b	87.7%	13.9%	3.9%	91.7%	25.6%	3.4%
Total^bc	93.4%	63.3%	71.9%	92.6%	47.9%	50.0%

Repetitive content as identified by RepeatMasker. ^aNumber of sequences (percentage of total) within which repetitive content was found. ^bPercentage of the total number of bases within the consensus sequences of the given library. ^cAs a reference, annotated repetitive elements cover 48.1% of the bovine genome.

ISSN: 1471-2164