scPASU: A computational protocol for quantifying polyadenylation site usage and alternative polyadenylation from 3' scRNA-seq data.

Alexandra Krylova, Ninh B Le, Angela H Ting

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Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Alexandra KrylovaDepartment of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA. Electronic address: aekrylova@mdanderson.org.

Ninh B LeDepartment of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.

Angela H TingDepartment of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA. Electronic address: ahting@mdanderson.org.

Funding

High resolution transcriptome and gene regulatory mapping of human ureter and bladder across the lifespanU01DK131383 · NIDDK · CLEVELAND CLINIC LERNER COM-CWRU · PI LEE, BYRON H, TING, ANGELA H · 2021 to 2025

$2.4M

NIDDK NIH HHS U01 DK131383

6 · The paper itself

Abstract

3' single-cell RNA sequencing (scRNA-seq) captures polyadenylation (poly(A)) sites, enabling quantification of site usage per gene and cell. Here, we present scPASU (single-cell poly(A) site usage), a Snakemake workflow for quantifying poly(A) site usage and alternative polyadenylation from 3' scRNA-seq data. We describe steps for building a poly(A) site reference, generating a site-by-cell matrix per sample, and testing alternative polyadenylation (APA) between cell groups. This protocol is configurable for organism- and sample-specific parameters and supports discovery of poly(A) sites. For complete details on the use and execution of this protocol, please refer to Le et al.

Indexed as

Computational BiologyPolyadenylationRNA-SeqSequence Analysis, RNASingle-Cell AnalysisAnimalsHumansPoly ARNA, MessengerSingle-Cell Gene Expression AnalysisSoftwarePoly ARNA, MessengerBioinformaticsRNAseqSequence analysis

Identifiers

PMID42085187

DOI10.1016/j.xpro.2026.104544

PMCPMC13157062

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.