AUTHOR=Michalik Juraj , Niederlova Veronika , Stepanek Ondrej 

TITLE=IDEIS: a tool to identify PTPRC/CD45 isoforms from single-cell transcriptomic data

JOURNAL=Frontiers in Immunology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1446931

DOI=10.3389/fimmu.2024.1446931

ISSN=1664-3224

ABSTRACT=<p>Single-cell RNA sequencing (scRNA-seq) methods are widely used in life sciences, including immunology. Typical scRNA-seq analysis pipelines quantify the abundance of particular transcripts without accounting for alternative splicing. However, a well-established pan-leukocyte surface marker, CD45, encoded by the <italic>PTPRC</italic> gene, presents alternatively spliced variants that define different immune cell subsets. Information about some of the splicing patterns in particular cells in the scRNA-seq data can be obtained using isotype-specific DNA oligo-tagged anti-CD45 antibodies. However, this requires generation of an additional sequencing DNA library. Here, we present IDEIS, an easy-to-use software for CD45 isoform quantification that uses single-cell transcriptomic data as the input. We showed that IDEIS accurately identifies canonical human CD45 isoforms in datasets generated by 10× Genomics 5’ sequencing assays. Moreover, we used IDEIS to determine the specificity of the <italic>Ptprc</italic> splicing pattern in mouse leukocyte subsets.</p>