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Updated: Jan 10, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics.

Patricia Hayes Doyle^1,2, Madeline L Page^1,2,3, J Anthony Brandon^1,2,3

¹Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.

Biorxiv : the Preprint Server for Biology

|November 24, 2025

Summary

This summary is machine-generated.

Long-read single-cell sequencing reveals novel RNA isoforms in human immune cells. This advanced method maps the full "isonome" for better understanding of cellular diversity and disease.

Keywords:

Gene Genomics Isoform Long-read Nanopore ONT PBMC PIPseq RNA blood immune isonome nanopore sequencing scRNA-seq sequencing

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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations

Published on: October 25, 2018

Area of Science:

Genomics
Molecular Biology
Immunology

Background:

Short-read sequencing limits isoform-level analysis of cellular diversity.
Understanding cell-type-specific gene expression requires isoform resolution.
Long-read sequencing offers a path to deeper biological insights.

Purpose of the Study:

To generate the largest long-read single-cell dataset of human peripheral blood mononuclear cells (PBMCs) to date.
To profile isoform usage across immune cell types and discover novel isoforms.
To integrate isoform discovery with marker gene expression for functional context.

Main Methods:

Utilized a modified, microfluidic-free PIPseq workflow.
Adapted a computational pipeline for Oxford Nanopore long-read sequencing.
Generated and analyzed a large-scale long-read single-cell dataset of human PBMCs.

Main Results:

Identified 128 novel isoforms from known and new genes, with cell-type-specific patterns.
Characterized marker gene isoform expression across various immune cell types.
Discovered non-canonical protein-coding variants and novel transcripts (e.g., from GZMB, CD3G, CMC1, LYAR) enriched in specific cell populations.

Conclusions:

Long-read single-cell sequencing enhances the study of isoform signatures within their biological context.
This approach provides a powerful tool for mapping the isoform landscape (isonome) in health and disease.
The findings expand the utility of long-read single-cell technologies for detailed cellular and molecular investigations.