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

BMC Genomics

Table 1 Per-library metrics

	Blastocyst embryos			Elongation embryos
Methods	Me-RDA	HMe-RDA	HELP cocktail	Me-RDA	HMe-RDA	HELP cocktail
Methods	Msp/Hpa	FspBI/BfaI	HELP cocktail	Msp/Hpa	FspBI/BfaI	HELP cocktail
Average raw read length (base pair)^a	285 ± 121	235 ± 142	257 ± 113	274 ± 132	115 ± 87	241 ± 142
Reads with internal genomic digestion site^b	17 429 (6.2%)	3547 (4.8%)	23 396 (10.0%)	15,245 (7.9%)	2134 (3.0%)	9037 (4.1%)
Putative methylated restriction sites within CpG Islands^c	1198 (33.4%)	455 (2.1%)	313 (1.7%)	899 (34.8%)	546 (3.5%)	1583 (4.0%)

^aWith standard deviation. ^bNumber of cleaned reads (percentage of all cleaned reads) containing an intact site for a methyl-insensitive restriction endonuclease more than 10 nucleotides from the ends. Such sites are indicative of incomplete genomic cleavage. ^cThe percentage of putative methylated restriction sites within CpG islands over the total number of sites identified for this library. As a reference, CpG islands cover 1.9% of the bovine genome.

ISSN: 1471-2164