Reanalysis of the combinatorial optical pooled CRISPR screen (CROPseq-multi) from Walton et al. (Nature Biotechnology), processed with brieflow v1.2.0.
| Parameter | Value |
|---|---|
| Cell line | HeLa (doxycycline-inducible Cas9) |
| Library | CROPseq-multi-v2 (CSMv2), 6,000 constructs |
| Targets | 360 essential genes + 280 gene combinations (combinatorial CRISPR-KO) |
| Guides per gene | 4 |
| Plates | 2 (9 wells total) |
| SBS cycles | 15 (3 iBAR1 recombination + 12 iBAR2 mapping) |
| Phenotype rounds | 2 (10 markers, 9 final channels) |
| Phenotype markers | DAPI, Ki-67, COX IV, Cleaved Caspase-3, WGA, α-Tubulin, Vimentin, γH2AX, Phalloidin |
| Microscope | Nikon Ti2 inverted epifluorescence |
Raw data was processed end-to-end with brieflow, covering preprocessing, SBS decoding, phenotype feature extraction, merge, aggregate, and clustering steps. Configuration notebooks and Slurm scripts are in analysis/.
Raw imaging data (ND2 format) is archived at BioImage Archive S-BIAD3248. Brieflow outputs are stored at /lab/ops_analysis_hdd/cheeseman/etna-analysis/. Source data used for figure generation is in analysis/source_data/.
Citation will be added upon publication.