Multiplexed single-cell characterization of alternative polyadenylation regulators (HEK293FT & K562 Perturb-seq data)

<p>This site provides access to datasets from the CPA-Perturb-seq <a href="https://www.biorxiv.org/content/10.1101/2023.02.09.527751v1">manuscript</a> 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 <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>The files include:</p> <p>1. CPA_K562.Rds : Seurat object containing the K562 CPA-Perturb-seq dataset&nbsp;</p> <p>2. CPA_K562_fragments.tsv.gz : Fragment file for the K562 dataset&nbsp;</p> <p>3. CPA_K562_fragments.tsv.gz.tbi : Fragment file index for the K562 dataset&nbsp;</p> <p>&nbsp;</p> <p>R code below:</p> <pre><code>library(PASTA) k562 &lt;- readRDS("CPA_K562.Rds") # Add fragments for plotting&nbsp; Fragments(k562) &lt;- CreateFragmentObject(path = "download/CPA_K562_blocks.tsv.gz", cells = Cells(k562)) # visualize polyA site usage PolyACoveragePlot(k562, region ="chr7-26212195-26213351")</code></pre>