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Updated: Jun 3, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing.

Roozbeh Dehghannasiri¹, Marek Kokot², Alexander L Starr³

¹Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA.

Biorxiv : the Preprint Server for Biology

|January 7, 2025

Summary

This summary is machine-generated.

sc-SPLASH is a new bioinformatics pipeline for analyzing single-cell RNA sequencing data. It discovers novel transcriptomic diversity, including gene expression and mutations, without relying on reference genomes.

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Last Updated: Jun 3, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

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Published on: May 23, 2018

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Published on: August 11, 2011

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Standard single-cell RNA sequencing (scRNA-seq) methods often miss transcriptomic diversity due to reliance on gene models and reference genomes.
Mechanisms like alternative splicing and V(D)J recombination generate significant transcriptomic variation not captured by current analyses.
Imperfect reference genomes can lead to the omission of relevant biological sequences.

Purpose of the Study:

To introduce sc-SPLASH, an efficient pipeline for reference-free transcriptomic discovery in barcoded single-cell and spatial transcriptomics data.
To provide BKC, an optimized module for preprocessing and k-mer counting in barcoded data, as a standalone tool.
To demonstrate the utility of sc-SPLASH in uncovering diverse biological phenomena across various species.

Main Methods:

Extension of the SPLASH framework for statistics-first, reference-free analysis.
Application to 10x Chromium (scRNA-seq) and 10x Visium (spatial transcriptomics) data.
Development of BKC module for preprocessing and k-mer counting in barcoded datasets.

Main Results:

sc-SPLASH successfully identified V(D)J recombination and cell-type-specific alternative splicing in human data.
Trans-splicing in tunicates (Ciona) and sequence variations, including tumor-specific somatic mutations, were detected in spatial datasets.
Novel secreted repeat proteins in immune-type cells of sponge (Spongilla) and tunicate (Ciona) were discovered, including genes absent from reference assemblies.

Conclusions:

sc-SPLASH offers a powerful, reference-free alternative for exploring transcriptomic diversity in single-cell and spatial data.
The pipeline is effective in discovering known biological processes and novel sequences across diverse organisms.
sc-SPLASH enhances the scope of transcriptomic analysis, particularly for non-model organisms and complex biological variations.