Cytos Assay Overviews
Cytos™ cell screening enables multimodal data generation on the AVITI24™ System.
Your Cytos assay selection decides which modalities you capture: cell paint, protein, guide RNA, 3' transcriptome, or a combination. Choose an assay in the table. Then follow the Cytos End-to-End Workflows map to create a custom design in ElemBio Cloud, plan the run, run 3' analysis when the assay needs it, and analyze with an agent.
| Assay | What it captures | Overview |
|---|---|---|
| Optimization | Cell paint only, before a full experiment | Optimization overview |
| Protein screening | Cell paint and up to 20 protein targets | Protein screening overview |
| Optical pooled screening | Cell paint and guide RNA, with optional protein | Optical pooled screening overview |
| 3' Transcriptome | Cell paint and 3' transcriptome, with optional protein | 3' transcriptome overview |
| Multimodal pooled screening | Cell paint, guide RNA, and 3' transcriptome, with optional protein | Multimodal pooled screening overview |
Optimization
Use the Cytos Onboard Optimization Kit to run a cell paint-only run on the AVITI24 System. Morphology features from cell paint fluorescence imaging include: cell membrane, nucleus, actin, and mitochondria. Optimization runs verify seeding density, surface adherence, staining, segmentation, and flow cell handling before you commit to a full multiomics experiment.
Optimization runs use the Cytos Onboard Optimization Kit directly and do not require a custom design in ElemBio Cloud Custom Designer™. Set up the planned run on Optimization run.
User guides
Protein screening
The Cytos Protein Kit captures cell paint and up to 20 custom protein targets. Use the Cytos protein assay to screen up to 20 custom antibodies to optimize your custom protein protocol before pairing protein with a Cytos RNA run for guide RNA or 3' transcriptome analysis.
The AVITI24 System images each protein target by immunofluorescence alongside the cell paint channels (cell membrane, nucleus, actin, and mitochondria), so morphology and protein expression come from the same cell.
User guides
Optical pooled screening
The Cytos Optical Pooled Screening Kit reads guide RNA optically from pooled CRISPR screens while capturing cell paint from the same cell. This assay covers optical pooled screening (OPS) alone and the optional protein add-on.
OPS links each guide RNA to the morphology of the cell that carries the guide. Each cell's perturbation is read in place without separate readouts. You can pair this assay with the Cytos Protein Kit to include cell paint, protein, and optical pooled screening in the same sample.
User guides
- Cytos Sample Preparation & Optimization User Guide (MA-00094)
- Cytos Protein User Guide (MA-00095)
- Cytos Optical Pooled Screening User Guide (MA-00096)
- Tutorial: Analyzing an optical pooled CRISPR screen
3' Transcriptome
The Cytos 3' Transcriptome Kit captures cell paint and 3' polyadenylated transcripts from the same cell. This assay covers the 3' transcriptome-only workflow and the optional protein add-on.
The AVITI24 System determines the sequencing batches and the cycles per batch automatically, so the 3' transcriptome module needs no customization in your design. You can pair this assay with the Cytos Protein Kit to include cell paint, protein, and 3' transcriptome in the same sample.
User guides
- Cytos Sample Preparation & Optimization User Guide (MA-00094)
- Cytos Protein User Guide (MA-00095)
- Cytos 3′ Transcriptome User Guide (MA-00098)
- Cytos Cell Screening analysis workflow
- Tutorial: Measuring a 3′ treatment response
- Tutorial: Clustering cells with Python
Multimodal pooled screening
The Cytos Multimodal Pooled Screening (MPS) Kit combines 3' transcriptome and optical pooled screening (OPS) into a single run, so morphology, guide RNA, and transcriptome are spatially located in the same run dataset. This assay covers guide RNA (OPS), 3' transcriptome, and the optional protein add-on.
Because all modalities are measured on the same fixed cells, each guide RNA assignment is linked to the morphology and the 3' expression profile of the cell that carries the guide. You can pair this assay with the Cytos Protein Kit to include cell paint, protein, optical pooled screening, and 3' transcriptome in the same sample.
User guides
- Cytos Sample Preparation & Optimization User Guide (MA-00094)
- Cytos Protein User Guide (MA-00095)
- Cytos 3′ Transcriptome User Guide (MA-00098)
- Cytos Multimodal Pooled Screening User Guide (MA-00097)
- Cytos Cell Screening analysis workflow
- Tutorial: Measuring a 3′ treatment response
- Tutorial: Analyzing an optical pooled CRISPR screen