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Table 1 Per-library metrics

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

  Blastocyst embryos Elongation embryos
Methods Me-RDA HMe-RDA HELP cocktail Me-RDA HMe-RDA HELP cocktail
Msp/Hpa FspBI/BfaI Msp/Hpa FspBI/BfaI
Average raw read length (base pair)a 285 ± 121 235 ± 142 257 ± 113 274 ± 132 115 ± 87 241 ± 142
Reads with internal genomic digestion siteb 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 Islandsc 1198 (33.4%) 455 (2.1%) 313 (1.7%) 899 (34.8%) 546 (3.5%) 1583 (4.0%)
  1. 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.