Origin & ancestral clones
Combine genomic relationships and normal epithelial lineage signals to formulate—not prove—cell-of-origin hypotheses.
WELLDR-SEQ · CELL 2025
The same cell.
Clone and state, connected.
Paired DNA and RNA measurements in assessed fresh tissue provide cell-level evidence for clone–phenotype relationships.
SAME CELL. TWO MOLECULAR READOUTS.
Distinguish similar expression
from shared genomic ancestry.
RNA describes state; DNA provides copy-number and clonal evidence. Directly paired measurements preserve their cell-level correspondence.
12ER+ breast tumors in the study
33,646Single cells analyzed
DNA + RNAPaired readouts from the same cell
These describe the Cell 2025 study, not pan-cancer validation or per-project cell-yield guarantees.
Open figure ↗THE PAIRED WORKFLOW
Not just another assay.
A preserved relationship.
DNA and RNA are separately barcoded in the nanowell workflow, preserving same-cell identity. Analysis centers on genome-wide low-pass CNA and transcriptional readouts.
DNA
Copy-number structure
Genomic subclones
RNA
Expression programs
Cell states
PAIR
Clone–phenotype relationships
Dosage associations
QUESTIONS WORTH GOING DEEPER
Which questions need DNA as well?
Not every expression difference follows a copy-number change. Define subclones first, then examine states and candidate mechanisms.
CNA & gene dosage
Compare copy number and expression within paired cells and subclones to prioritize candidates for functional validation.
Cell state & treatment studies
With appropriate pairs and controls, explore the contributions of clonal selection and transcriptional plasticity.
PUBLISHED STUDY · GENE DOSAGE
How do copy number
and expression align?
The supplied Cell 2025 materials report near-linear expression associations for about 56% of CNA segments in that study. This illustrates paired analysis—not a universal dosage effect for every gene.
Follow-up may include genetic perturbation, organoid experiments or independent cohorts. Same-cell association alone does not replace causal experiments.
Read the research interpretation
Open figure ↗SAMPLE & DESIGN NOTES
Agree the material before the assay.
Which samples are suitable?
This page is based on the published fresh solid-tumor study. Other preservation methods and tissue types require assessment; archived FFPE is not assumed compatible with this DNA+RNA workflow.
Can it complement existing scRNA data?
Discuss additional DNA evidence and validation. Old scRNA and newly measured DNA from different cells remain cross-sample or cross-cell integration, not directly measured same-cell data.
Will it guarantee a rare clone or resistance target?
No. Rare-clone observation depends on effective cell count, background, quality and thresholds. Mechanistic candidates require independent validation.
LET’S BUILD YOUR STUDY
Start with a question worth answering.
Bring your sample type, research question and existing data. Let’s find the right starting point.