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

This site provides access to datasets from the CPA-Perturb-seq manuscript Kowalski*, Wessels*, Linder* et al., including PBMC data to replicate analyses in Figure 6. 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. 

To replicate the analysis in Figure 6, in which we analyze a dataset of circulating human peripheral blood mononuclear cells,  we provide a vignette available here. To following files are used:

1. matrix.mtx: 10X file containing RNA for PBMC dataset

2. barcodes.tsv: 10X file containing barcodes for PBMC dataset

3. genes.tsv: 10X file containing genes for PBMC dataset

4. PBMC_meta_data.csv: meta data for PBMC dataset

5. PBMC_pA_counts.tab.gz: Counts file containing polyA quantification for PBMC dataset

6. PBMC_fragments.tsv.gz: Fragment file to visualize the PBMC dataset.

7. PBMC_fragments.tsv.gz.tbi: Fragment file index for the PBMC dataset.    

8. PBMC_polyA_peaks.gff: Gff file containing location of polyA site read regions.

9. human_PAS_hg38.txt: Text file containing information from polyAdbv3 resource.