Cytos™ Cell Screening

Cytos is the same cell multiomics workflow for CRISPR and drug screening on AVITI24™ . In a single automated run, Cytos captures morphology, protein expression, guide RNA, and 3’ transcriptome from the same cell—so a hit isn't just a hit, it's a story you can act on immediately.

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Cytos Cell Screening with Element Biosciences

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See the biology behind every screen

Whether you're unraveling the effects of a CRISPR perturbation or determining the mechanism of action of a compound, you're asking the same thing: what’s actually happening inside the cell? Cytos answers that in a single run with guide RNA, morphology, protein, and transcriptome, captured together, all with no library prep and less than an hour of hands-on time.

CRISPR & optical pooled screening

Pair direct guide RNA sequencing with same-cell morphology, protein, and transcriptome so you see not just which gene was perturbed, but everything that happened because of it.

See how it performs in CRISPR screening

Phenotypic drug discovery

Resolve efficacy, dose response, and mechanism of action from the same treated cells. Cytos brings transcriptome, protein, and morphology together in every experiment, so you learn not just that a compound worked, but why.

Explore drug screening applications

Rich morphology and multiomic readouts

Morphology

Protein

3' Transcriptome

Guide RNA

Morphology (Cell Paint)

Watch how a perturbation or treatment change the cell itself.

Multiplexed imaging across 4 cell morphology markers: cell membrane, nucleus, actin, mitochondria.
Automated, onboard segmentation and feature extraction—no manual image analysis pipeline.
Add custom immunofluorescent morphology markers.

Protein

Track downstream expression, localization, or pathway activation.

Up to 20-plex immunofluorescent based readouts, including fixed panels and custom targets.
Intensity-based detection, built for dynamic range across expression levels.
No conjugation or barcoding required to add a custom target.

3' Transcriptome

Catch a pathway-level response that a targeted panel could miss.

Unbiased, whole transcriptome sequencing via Direct In Sample Sequencing with no library prep and no separate NGS run.
The readout that explains why a hit or a compound behaved the way it did, not just that it did.

Guide RNA

See exactly which perturbation each cell received, read directly inside the cell.

DISS reads guide identity in place, so a hit is never disconnected from what happened next.
High-confidence guide assignment, so you can screen 10s-100k guides.

Product Configurations

	Protein (up to 20-plex, including custom)	Cell Paint (membrane, nucleus, actin, mitochondria)	Guide RNAs (10s-10ks)	3' Transcriptome (poly-A)
Cytos Optical Pooled Screening	✅	✅	✅
Cytos Multimodal Pooled Screening	✅	✅	✅	✅
Cytos 3' Transcriptome	✅	✅		✅

How it works

Cytos captures guide RNA, morphology, protein, and transcriptome directly from the same intact cell using Direct In Sample Sequencing with no library prep, no separate NGS run. The moment a run finishes, ElemBio Catalyst™ automatically launches secondary analysis, including alignment and assignment. From there, view every modality with our visualization tools or perform pathway-level or tertiary analysis.

By the numbers

in a dual sided run

custom protein and morphology markers

in a dual-sided run

Cytos is Element's same-cell multiomics workflow for CRISPR and phenotypic screening on AVITI24. In a single automated run, it captures cell morphology, protein, guide RNA, and 3' transcriptome from the same cell, using Direct In Sample Sequencing to remove the library prep step entirely.
No. Cytos configurations span guide RNA and morphology (OPS) up through guide RNA, morphology, protein, and full 3' transcriptome (MPS), so you can match the readout to your question without switching instruments or workflows.
With a streamlined workflow, Cytos provides speed to insight in every screen. Multimodal readouts are automated onboard AVITI24 with less than an hour of offboard prep, no separate NGS prep, and run times as low as 1 day.
No, Direct In Sample Sequencing captures guide RNA and transcriptome sequences directly from fixed cells onboard AVITI24, removing the separate library prep and sequencing run that most screening workflows require.
Cytos is our improved, next-generation multiomics workflow for AVITI24. Direct In Sample Sequencing now powers 3' whole transcriptome sequencing and native in situ guide RNA sequencing. Protein readouts use intensity-based immunofluorescent detection instead of spot-based counting.

Product Name	880-00004
Product Name	895-00060

Cytos™ Cell Screening