Which populations are present?
Use expression features, markers and reference information to study cellular composition and compare populations across samples.
CELL STATES, IMMUNITY & REGULATION
From cellular composition to states and regulation.
Cell identities and states help shape tissue and population function. Single-cell transcriptomics provides an expression-level view, while appropriate chromatin assays add evidence relevant to gene regulation.
QUESTIONS TO EXPLORE
Questions for cell-state research.
Which expression programs change?
Compare conditions or sample groups within cell populations to investigate immune responses, development, stress and other relevant states.
What regulatory clues emerge?
Use an appropriate ATAC assay to examine chromatin accessibility and complement expression analysis, with the relationship between experiments explicitly defined.
DISTINCT READOUTS, DISTINCT QUESTIONS
What expression reveals, and what chromatin adds.
RNA: differences in expression
Organize transcript information using cell barcodes and molecular identifiers to study composition, expression and cell states. The selected workflow defines what can be measured.
ATAC: evidence from accessibility
Chromatin accessibility provides another molecular perspective. Accessibility alone does not establish a specific regulatory effect or causal relationship.
RNA and ATAC may involve separate experiments. A same-cell joint workflow requires separate assessment and is currently under optimization.
STUDY DESIGN
Experimental design for cell-state studies.
- 01
Match the workflow to the hypothesis
Distinguish broad expression profiling, targeted transcript questions and chromatin-accessibility studies before choosing the assay.
- 02
Consider preparation effects
Discuss dissociation, cell condition and sample handling, documenting factors that may alter cell proportions or induce stress-associated expression.
- 03
Plan replicates & batches
Plan biological replicates and experimental batches. A large number of cells is not equivalent to a large number of independent biological samples.
- 04
Interpret states in context
Interpret annotations and differences using biological context, reference information and follow-up validation. State labels should be traceable to the evidence supporting them.
ANALYTICAL FOCUS
Analysis and functional validation.
Composition & states
Organize findings around quality assessment, population grouping, annotation, differential expression or pathway-related analyses. The sample design and service scope determine the analysis.
Association needs functional follow-up
Changes in expression or accessibility can suggest mechanisms, but do not alone establish cell interactions, antigen specificity or regulatory causality. Functional questions require follow-up experiments.
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