Table 2.

Bioinformatics analysis pipeline for the identification of putatively methylated sites

	Blastocyst embryos			Elongation embryos			All
Method	Me-RDA	HMe-RDA	HELP cocktail	Me-RDA	HMe-RDA	HELP cocktail
	Msp/Hpa	FspBI/BfaI		Msp/Hpa	FspBI/BfaI
Raw reads from library	313 330	179 105	242 864	208 963	94 961	243 874	1 283 097
Cleaned readsa	281 619	72 855	234 149	192 163	71 459	218 874	1 071 119
Validated readsb	N/A	N/A	46 835	N/A	N/A	50 462	N/A
Consensus sequencesc	33 123	29 416	31 604	25 616	24 963	41 784	186 506
Sequences with genomic alignmentsd	28 941	25 360	25 519	18 944	14 978	37 759	151 501
Sequences with unique alignmente	1890	11 772	14 712	1317	8858	30 587	69 136
Putative methylated restriction sitesf	3634	21 352	18 810	2584	15 714	39 367	101 461

^aNumber of reads left after cleaning with SeqClean. Reads smaller than 25 nt after adapter trimming were discarded. ^bFor HELP, number of reads with an internal HpaII, AciI or HinP1I restriction site. ^cNumber of consensus sequences after clustering with a 97% identity threshold. ^dNumber of consensus sequences with a BLAT genomic alignment with 92% identity over 92% of the length of the transcript. ^eNumber of consensus sequences for which a single alignment fits the above criteria. ^fNumber of potentially methylated sites identified in the genome through the alignment and extension of reads. N/A = not applicable.