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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: Apr 11, 2026

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

BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing.

Jamie Bregman¹, Calen Nichols¹, Rajeev Ramisetti¹

¹Genome Regulation and Cell Signalling Program, The Wistar Institute, PA.

Biorxiv : the Preprint Server for Biology

|April 10, 2026

Summary

This summary is machine-generated.

BenchDrop-seq offers a practical benchtop platform for single-cell long-read RNA sequencing, enabling full-length transcript analysis at scale. This method overcomes previous limitations, making advanced transcriptomics accessible for routine experiments.

Keywords:

Long-read sequencing Oxford Nanopore Technology RNA-seq quantification Single-cell RNA-seq Transcript Isoforms

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Last Updated: Apr 11, 2026

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

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Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Single-cell long-read RNA sequencing (scLong-RNA-seq) provides direct measurement of full-length transcripts.
Current scLong-RNA-seq methods face challenges in scalability due to microfluidics, specialized equipment, and high costs.

Purpose of the Study:

To develop a practical and accessible benchtop platform for scLong-RNA-seq.
To enable high-throughput, isoform-resolved transcriptomic measurements from individual cells.

Main Methods:

BenchDrop-seq utilizes particle-templated partitioning for single-cell barcoding.
The platform integrates with Oxford Nanopore sequencing for full-length transcript capture.
An open-source analysis pipeline facilitates barcode recovery, alignment, and quantification.

Main Results:

BenchDrop-seq demonstrates high barcode recovery and accurate gene quantification.
The platform successfully identifies cell-type-specific transcript usage in heterogeneous tissues.
Isoform-resolved measurements are achieved from thousands of cells using standard lab equipment.

Conclusions:

BenchDrop-seq establishes a practical framework for scLong-RNA-seq, reducing experimental barriers.
The platform enables routine single-cell experiments with transcript-level analysis capabilities.
This advancement makes advanced transcriptomic analyses more accessible to researchers.