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

<p>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 <a href="https://github.com/satijalab/PASTA">PASTA</a> (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.&nbsp;</p> <p>&nbsp;</p> <p>To replicate the analysis in Figure 6, in which we analyze a dataset of circulating human peripheral blood mononuclear cells,&nbsp; we provide a vignette available <a href="http://www.satijalab.org/seurat/articles/pasta_vignette.html">here</a>. To following files are used:</p> <p>&nbsp;</p> <ol> <li> <p>matrix.mtx: 10X file containing RNA for PBMC dataset</p> </li> <li> <p>barcodes.tsv: 10X file containing barcodes for PBMC dataset</p> </li> <li> <p>genes.tsv: 10X file containing genes for PBMC dataset</p> </li> <li> <p>PBMC_meta_data.csv: meta data for PBMC dataset</p> </li> <li> <p>PBMC_pA_counts.tab.gz: Counts file containing polyA quantification for PBMC dataset</p> </li> <li> <p>PBMC_fragments.tsv.gz: Fragment file to visualize the PBMC dataset.</p> </li> <li> <p>PBMC_fragments.tsv.gz.tbi: Fragment file index for the PBMC dataset.&nbsp;&nbsp; &nbsp;</p> </li> <li> <p>PBMC_polyA_peaks.gff: Gff file containing location of polyA site read regions.</p> </li> <li> <p>human_PAS_hg38.txt: Text file containing information from polyAdbv3 resource.&nbsp;</p> </li> </ol>