CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators (Perturb-seq data)
DOI10.5281/zenodo.7619593Zenodo7619593MaRDI QIDQ6677941FDOQ6677941
Dataset published at Zenodo repository.
Isabella Mascio, Yuhan Hao, Rahul Satija, Madeline Kowalski, Anshul Kundaje, Saket Choudhary, Hans-Hermann Wessels, Carol Dalgarno, Austin Hartman, Johannes Linder
Publication date: 8 February 2023
Copyright license: Creative Commons Attribution 4.0 International
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")
This page was built for dataset: CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators (Perturb-seq data)
