Fig. 1

SCL-exo of a 5hmC-containing DNA standard. a Schematic representation of the SCL-exo procedure. Note that, for the sake of clarity, only single-stranded DNA is shown. b Sequence of the forward strand of a 224-bp hydroxymethylated DNA standard obtained by PCR amplification of mm8 chr3:93,697,590-93,697,813, using 5hmdCTP instead of dCTP. Sequences corresponding to the primers are underlined and do not contain 5hmCs. All other cytosines were hydroxymethylated. Positions of the three first 5hmCs of the forward strand and of the four first 5hmCs of the reverse strand have been numbered 1, 2, 3 and 4, 5, 6, 7, respectively. c Cytosine density along read length (10,000 reads for each strand). d Number of reads covering each position along the DNA standard for both forward and reverse strands. Numbering on the graph indicates the 5hmCs identified 1, 2, 3 and 4, 5, 6,7 in (b). e Coverage of each C of the DNA standard found within 10 bases from the start of all reads. f Close-up view of the signal shown within the blue box in (e) and associated to the first 60 bases of the forward strand. The sequence is shown below and 5hmCs have been marked by asterisks