Supplementary Figure 2: Development and validation of STEM-seq.
From: Dynamic epigenomic landscapes during early lineage specification in mouse embryos
a Schematic of STEM-seq procedure. Genomic DNA (or lysed cells) is first subjected to bisulfite conversion, followed by sequencing library preparation using TELP, a highly sensitive single-strand DNA amplification and library preparation method. Briefly, the purified converted DNA is tailed by poly C, followed by extension with a biotinylated poly G containing primer. The extension product is ligated to an adaptor followed by PCR amplification for sequencing library preparation (See Methods for details). b A UCSC genome browser snapshot shows comparison of mESC methylomes determined by STEM-seq and MethylC-seq using various amounts of DNA or cells in two mESC lines (TT2 and R1) near the Hoxa gene cluster. CpG islands (CGIs) in this region are also shown. c Scatterplots show the comparison of mESC methylation levels between those determined by STEM-seq and MethylC-seq (2kb bin), or between replicates of STEM-seq data across the whole genome. Pearson’s correlation coefficients are also shown. d Comparison of average CG methylation levels in mESCs at different genomic elements between those determined by STEM-seq using 10ng or 100ng DNA and MethylC-seq. e A similar plot as d for STEM-seq using 500 mESCs with two replicates. Please note that different mESC lines were unintentionally used in d (TT2) and e (R1)
