You Found a CRISPR Hit.
Now What Actually Changed in the Cell?

CRISPR screens can identify genes associated with a phenotype, but guide enrichment alone does not explain the biological consequences of each perturbation. Single-cell multimodal screening can connect guide identity with morphology, protein expression and transcriptome-wide responses within the same cells.

Moving Beyond Hit Identification

Traditional pooled CRISPR screens are extremely effective for identifying genes associated with survival, resistance, signaling or other selectable phenotypes.

But once a hit is identified, new questions emerge:

How did the perturbation change cell morphology?

Which downstream proteins changed?

Which signaling pathways were activated or suppressed?

What happened across the transcriptome?

Answering these questions requires linking perturbation identity directly to molecular and cellular phenotypes.

Four Biological Layers From the Same Cell

Guide RNA
Identify the genetic perturbation carried by each cell.

Morphology
Measure changes in cellular structures including membrane, nucleus, actin and mitochondria.

Protein
Track protein abundance, localization and pathway-associated changes.

3′ Transcriptome
Capture unbiased transcriptional responses beyond predefined targeted gene panels.

Why Same-Cell Measurement Matters

When RNA, protein and imaging assays are performed on separate samples, researchers compare population-level averages.

Measuring multiple modalities in the same cells enables a direct connection between perturbation and consequence.

A single experiment can therefore ask whether a specific knockout is associated with a transcriptional response, altered protein expression and a matching morphological phenotype.

A Real Multimodal Pooled Screening Dataset

An Element Biosciences Cytos™ dataset combined guide sequencing, 3′ transcriptome profiling, Cell Paint and 4-plex protein detection in baseline and TNF-α stimulated cells.

Across six replicates per condition, 258,277 cells were profiled and 87% of cells were assigned to a guide RNA.

TGFBR2 knockout cells showed loss of the receptor transcript together with reduced expression of canonical TGF-β targets including PMEPA1, TGFBI, CDH2, IGFBP7 and S100A4, accompanied by a corresponding morphological phenotype.

Why Include Protein?

Transcript abundance does not always predict protein abundance, and RNA measurements cannot directly capture many biologically important features such as phosphorylation or protein localization.

Cytos™ provides immunofluorescence-based protein readouts up to 20-plex, including fixed panels and custom targets.

High-quality validated antibodies therefore become an important component of multimodal phenotype interpretation.

ABclonal × Element Biosciences

ABclonal and Element Biosciences are bringing antibody reagents together with AVITI24™-based spatial and single-cell multiomic workflows.

Validated antibodies and biotinylated antibody options can support protein profiling alongside genetic and transcriptional measurements.

The broader opportunity is to connect genetic perturbation → RNA response → protein phenotype → cell morphology within a unified experimental framework.

The Same Concept Extends to Drug Screening

Multimodal analysis can also provide richer phenotypic information for compound screening.

Instead of relying on a single viability endpoint, treated cells can be evaluated for dose-dependent morphology, protein responses and transcriptome-wide pathway changes.

This can help move a screening result from “the compound worked” toward “this is how the compound changed the cell.”

Applications for Multimodal Screening

✓ Genome-wide and focused CRISPR screens

✓ Optical pooled screening

✓ Functional genomics

✓ Phenotypic drug discovery

✓ Mechanism-of-action studies

✓ Signaling pathway analysis

✓ Protein localization studies

✓ Cellular morphology profiling

✓ Perturbation-to-phenotype mapping

Planning a CRISPR, Spatial Proteomics or Single-Cell Multiomics Study?

Dana Bioscience can help identify research reagents and workflow options for CRISPR screening, spatial and single-cell protein profiling, validated antibodies and multimodal functional genomics.

Share your target, sample type, CRISPR library, protein markers and desired biological readouts, and we can help evaluate appropriate research products and workflow options.