Simultaneous DNA + Protein + CpG Methylation Analysis on Tapestri^®

A workflow optimized for human samples that reveals clonal architecture, epigenetic states, and differentiation all in the same cells.

GET STARTED

Key Benefits

Bulk assays and plate-based methods miss rare clones and can’t connect genotype ↔ epigenetic state ↔ lineage in the same cells. Aging and disease reshape hematopoiesis through subtle clonal dynamics that require high cell counts and multi-omic context to see.

With CpG Methylation Profiling on Tapestri, you can:

Reveal clonal hematopoiesis earlier by pairing single-cell DNA variants/CNVs with CpG methylation, enabling the ability to detect early heme malignancies.
Track lineage trajectories retrospectively in human samples with no transgenics required.
Confidently identify and prioritize new therapeutic or monitoring targets with single-cell multi-omic insights.

Case Study

EPI-Clone study: Clonal tracing with somatic epimutations reveals dynamics of blood ageing.
(Adapted from Scherer M. et al., Nature 643, 478–487 (2025))

CpG analysis revealed age-dependent mutations, identifying both known and newly detected CH (clonal hematopoiesis) mutations.
Static CpG UMAPs overlaid with clonal structures showed methylation-based clustering aligned with known CH mutations.
Lineage tracing demonstrated that stable methylation patterns are less tied to transient differentiation states.

What You Can Uncover

Age‑linked epigenetic signatures tied to known and newly detected clonal hematopoiesis (CH) mutations.
Stable methylation states that illuminate clonal structure beyond transient differentiation signals.
Emergent SNVs with coordinated methylation + lineage shifts – that reveal clone‑specific targets to track.

Applications

Translational & clinical research teams monitoring clonal hematopoiesis (CH) / Acute Myeloid Leukemia (AML) / Multiple Myeloma (MM) risk, minimal residual disease (MRD), or therapy response.
Aging & stem-cell biology labs mapping differentiation potential across the lifespan.
Drug discovery groups prioritizing clone-specific vulnerabilities.
Therapy developers targeting the epigenome.

Workflow

Prepare single‑cell suspensions from human bone marrow or blood.
Tapestri DNA (+ Protein optional) to call SNVs/CNVs at single‑cell resolution.
Add methylation-sensitive endonuclease (scTAM-seq) to target informative CpG loci (bisulfite-free).
Analyze & visualize with UMAPs, clonal trees, and multi-omic overlays to quantify clonal architecture, methylation states, and trajectories.

Example Data

Figure 1: Single-cell DNA and CpG methylation maps showing clonal architecture and lineage composition. (Top) UMAPs display individual cells colored by specific genetic alterations: Loss of Y chromosome (LoY) (A.6, blue) and ASXL1 Q529X mutation (A.7, red), highlighting distinct clonal populations relative to wild-type cells (gray). (Bottom) Corresponding methylation-based cell type maps show lineage annotation according to CpG signature categories (Static CpGs, TBM/no mature, and T or B cells) for the same samples, as indicated in panels c and d at left.

Figure 1 adapted from Scherer M., Singh, I., Braun, M.M et al. Clonal tracing with somatic epmutations reveals dynamics of blood ageing. Nature 643, 478 (2025).

Selected references

Scherer M. et al., Nature (2025): Clonal tracing with somatic epimutations reveals dynamics of blood ageing.
Bianchi A. et al., Genome Biology (2022): scTAM‑seq enables targeted high‑confidence single-cell DNA methylation analysis.
Lareau C.A. et al., bioRxiv (2023): mtDNA features informing evolutionary and somatic fitness.

Simultaneous DNA + Protein + CpG Methylation Analysis on Tapestri®