CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators (Perturb-seq data)

This site provides access to datasets from the CPA-Perturb-seq manuscript Kowalski*, Wessels*, Linder* et al., including processed Perturb-seq datasets from HEK293FT and K562. We release these data as Seurat objects, where each object contains single-cell quantifications of gene expression (RNA assay), and in addition, quantifications of polyA site usage (polyA site assay). To explore these data, please install the PASTA (PolyA Site analysis using relative Transcript Abundance) package, which provides infrastructure and analytical tools to explore alternative polyadenylation at single-cell resolution. For each dataset, we also include a fragment file which enables visualization of read coverage plots across groups of cells. 

The files include:

1. CPA_HEK293FT.Rds: Seurat object containing the HEK293 CPA-Perturb-seq dataset 

2. CPA_HEK293FT_fragments.tsv.gz : Fragment file for the HEK293 dataset

3. CPA_HEK293FT_fragments.tsv.gz.tbi : Fragment file index for the HEK293 dataset

4. CPA_K562.Rds : Seurat object containing the K562 CPA-Perturb-seq dataset 

5. CPA_K562_fragments.tsv.gz : Fragment file for the K562 dataset 

6. CPA_K562_fragments.tsv.gz.tbi : Fragment file index for the K562 dataset 

R code below:

library(PASTA)

hek <- readRDS("CPA_HEK293FT.Rds")

# remove fragment file information
Fragments(hek) <- NULL
# Update the path of the fragment file 
Fragments(hek) <- CreateFragmentObject(path = "download/CPA_HEK293FT_fragments.tsv.gz", cells = Cells(hek))

# visualize polyA site usage
PolyACoveragePlot(hek, region ="7-26212195-26213351")