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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: Jul 16, 2025

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

A targeted sequencing extension for transcript genotyping in single-cell transcriptomics.

Lies Van Horebeek¹, Margaux David¹, Nina Dedoncker¹

¹Laboratory for Neuroimmunology, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.

Life Science Alliance

|September 11, 2023

Summary

This summary is machine-generated.

This study introduces a targeted sequencing method to combine genotyping with single-cell RNA sequencing. This approach enables the study of genetic variants

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Last Updated: Jul 16, 2025

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

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

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

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Single-cell RNA sequencing (scRNA-seq) lacks methods for high-throughput genotyping of specific genomic loci.
Understanding the functional impact of genetic variants at the single-cell level is crucial.

Purpose of the Study:

To develop and evaluate a targeted sequencing extension for droplet-based scRNA-seq.
To integrate transcript-level genotype information with gene expression data.
To enable the study of genetic variant impact on cellular transcriptomes.

Main Methods:

Extension of droplet-based scRNA-seq with targeted sequencing.
Processing of scRNA-seq and targeted sequencing data.
Evaluation of technical parameters (cDNA input, amplification cycles, sequencing depth).

Main Results:

Demonstrated a straightforward targeted sequencing extension for scRNA-seq.
Assessed the influence of technical parameters on transcript detection.
Showcased applications in somatic variant analysis and allele-specific expression studies.

Conclusions:

The targeted sequencing extension facilitates simultaneous analysis of genetic variants and transcriptomes.
This method aids in investigating the functional effects of genetic variation in single cells.
Potential to advance understanding of genotype-phenotype relationships at single-cell resolution.