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Fig. 2 | Genome Biology

Fig. 2

From: MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics

Fig. 2

Single cell transcriptome and epigenome data show common modes of variation. ad Single cell trajectories constructed by SLICER from RNA-seq, bisulfite sequencing, ATAC-seq, and H3K4me2 ChIP-seq of mESCs grown in serum. el Levels of important gene expression, DNA methylation, chromatin accessibility, and H3K4me2 markers across the trajectories. Note: We used SLICER for the analysis in this figure because it is a previously published method for constructing cell trajectories that allowed us to investigate the hypothesis that single cell transcriptome and epigenome measurements share common sources of variation. SLICER and MATCHER are completely separate methods; MATCHER does not rely on SLICER in any way; and SLICER could not be used to integrate multiple types of measurements as MATCHER does, because SLICER lacks the ability to generate unobserved cell measurements

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