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Related Experiment Video

Updated: Jun 9, 2025

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets
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IDEIS: a tool to identify PTPRC/CD45 isoforms from single-cell transcriptomic data.

Juraj Michalik1, Veronika Niederlova1, Ondrej Stepanek1

  • 1Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia.

Frontiers in Immunology
|October 24, 2024
PubMed
Summary
This summary is machine-generated.

IDEIS software quantifies CD45 isoforms from single-cell RNA sequencing data without extra libraries. This method accurately identifies immune cell subsets based on PTPRC gene splicing patterns.

Keywords:
CD45PTPRCT cellalternative splicinggene expressionimmunologyisoformsingle-cell RNA sequencing

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Area of Science:

  • Immunology
  • Computational Biology
  • Genomics

Background:

  • Single-cell RNA sequencing (scRNA-seq) is crucial in life sciences but often overlooks alternative splicing.
  • The PTPRC gene, encoding CD45, exhibits alternatively spliced variants critical for defining immune cell subsets.
  • Current methods for analyzing CD45 splicing variants require additional sequencing libraries, increasing complexity and cost.

Purpose of the Study:

  • To develop an accessible software tool, IDEIS, for quantifying CD45 isoforms directly from scRNA-seq data.
  • To enable detailed analysis of immune cell populations based on CD45 splicing heterogeneity.
  • To provide a cost-effective alternative to existing methods for CD45 variant analysis.

Main Methods:

  • Development of IDEIS, a user-friendly software tool.
  • Inputting standard scRNA-seq transcriptomic data into IDEIS.
  • Validation using 10× Genomics 5' sequencing assay datasets for human samples.
  • Application to mouse leukocyte subsets to analyze PTPRC splicing specificity.

Main Results:

  • IDEIS accurately identifies canonical human CD45 isoforms from scRNA-seq data.
  • The software successfully differentiates immune cell subsets based on PTPRC splicing patterns.
  • Demonstrated specificity of PTPRC splicing patterns across various mouse leukocyte populations.

Conclusions:

  • IDEIS offers a streamlined and efficient approach for CD45 isoform quantification using existing scRNA-seq data.
  • This tool enhances the analytical capabilities of scRNA-seq for immunological studies by incorporating splicing information.
  • IDEIS facilitates deeper insights into immune cell heterogeneity and function through PTPRC splicing analysis.