Single-cell targeted DNA methylation analysis of human B cells

This dataset demonstrates scTAM-seq, a method for profiling the methylation state of up to 600 CpGs in 10,000 cells with dropout rates of <7%. Besides CpG methylation, scTAM-seq also profiles the expression of select surface proteins in the same cells. We provide for each sample separate protein and methylation fastq and csv files. Here, scTAM-seq was applied to B cells from human peripheral blood and bone marrow. Overall design: scTAM-seq combines single-cell PCR in droplets (Mission Bio Tapestri platform) with the digestion of genomic DNA using the methylation-sensitive restriction enzyme HhaI. This enzyme selectively cuts unmethylated GCGC recognition sites, while leaving methylated sites intact. Hence, upon digestion of genomic DNA in barcoded single-cell droplets, amplicons containing targeted CpGs can only be amplified from methylated recognition sites. scTAM-seq can cover 600 CpGs in up to 10,000 cells, and can be combined with single-cell readouts of surface protein expression as well as somatic mutations. For this pilot study, we designed a panel of 592 amplicons, of which 424 contained CpGs showing dynamic DNAm during B-cell differentiation, i.e., CpGs differentially methylated between hematopoietic stem cells (HSCs), pre-B-cells, immature B-cells, naive B-cells and memory B-cells. The remaining amplicons serve as controls and include amplicons without HhaI recognition sites, as well as amplicons covering CpGs that are constitutively methylated or unmethylated in B-cells. We applied scTAM-seq to B-cells from bone marrow and blood while additionally profiling the expression of 46 cell-surface proteins by staining cells with oligonucleotide-tagged antibodies. For both samples, we generated data from two experimental conditions, one digested by HhaI and one undigested control. We obtained data for 5,340-9,583 cells passing quality filters.