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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: Jun 9, 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

Seq-Scope: repurposing Illumina sequencing flow cells for high-resolution spatial transcriptomics.

Yongsung Kim¹, Weiqiu Cheng², Chun-Seok Cho¹

¹Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.

Nature Protocols

|November 1, 2024

Summary

This summary is machine-generated.

Seq-Scope enhances spatial transcriptomics by repurposing Illumina sequencing for high-resolution gene expression analysis. This cost-effective method offers submicrometer resolution and rapid results for molecular biology and histology research.

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Last Updated: Jun 9, 2025

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

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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

Area of Science:

Genomics
Molecular Biology
Histology

Background:

Spatial transcriptomics enables gene expression profiling with spatial context.
Current methods face limitations in resolution, cost, and scalability.

Purpose of the Study:

To introduce Seq-Scope, a novel protocol for high-resolution spatial transcriptome analysis.
To overcome limitations of existing spatial transcriptomics technologies.

Main Methods:

Repurposing the Illumina NovaSeq 6000 platform for spatial transcriptomics.
Detailed protocol for tissue section preparation, library construction, and computational analysis.
Integration of histological imaging with transcriptomic data at submicrometer resolution.

Main Results:

Seq-Scope achieves submicrometer resolution and high capture efficiency.
The protocol enables rapid turnaround time (within 3 days) and cost-effectiveness.
Demonstrates precise annotation of histopathology alongside transcriptomic data.

Conclusions:

Seq-Scope provides a scalable and affordable solution for high-resolution spatial transcriptome analysis.
The method is adaptable across various biological tissues.
It serves as a valuable tool for molecular biology and histology researchers.