10X Chromium Single Cell CRISPR Screening Workflows with Voyager

The Chromium Single Cell CRISPR Screening from 10x Genomics enables researchers to assess the effects of CRISPR-mediated pertubations on cellular phenotypes and gene expression. The workflow relies on harvesting cells that have been transduced with CRISPR guides and stimulated before single cell preparation and library generation. Workflows typically include 2-5 sgRNAs per gene and 100-250 cells can be recovered per guide. Currently, the 5’ CRISPR screening assay is compatible with most pre-existing Cas9 guide RNA vectors while the 3’ assay requires a specific capture sequence for capture of the guide.

Getting Started

The vignettes below provide examples of processing raw data using a workflow that includes seqspec, gget, and kallisto/bustools to generate a count matrix. We process the output of various transcriptomics technologies into a SpatialFeatureExperiment(SFE) object for use with Voyager.

Vignette	Colab Notebook	Description
Preprocess raw data	Colab Notebook	Fetch reference data with gget, process raw data with seqspec, generate a count matrix with kallisto-bustools
Create a SFE object	Colab Notebook	Download data, create SFE object

Analysis Workflows

The analysis tasks include basic quality control, spatial exploratory data analysis, identification of spatially variable genes, and computation of global and local spatial statistics. Accompanying Colab notebooks are linked.

Vignette	Colab Notebook	Description
10X CRISPR Basic QC	Colab Notebook	Basic qc and preprocessing