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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: Oct 25, 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

SCITO-seq: single-cell combinatorial indexed cytometry sequencing.

Byungjin Hwang^1,2,3,4,5, David S Lee^1,2, Whitney Tamaki⁶

¹Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA.

|August 6, 2021

Summary

This summary is machine-generated.

SCITO-seq is a new workflow using splint oligonucleotides for DNA-barcoded antibody sequencing. This ultra-high-throughput method enables cost-effective single-cell protein and multimodal profiling for large-scale studies.

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Last Updated: Oct 25, 2025

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

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Published on: May 23, 2018

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

Published on: March 12, 2021

Area of Science:

Single-cell biology
Molecular biology
Biotechnology

Background:

Droplet-based single-cell sequencing (dsc-seq) profiles cell surface proteins but is costly.
Current dsc-seq methods are limited for clinical applications and large-scale screens due to high per-cell costs.

Purpose of the Study:

Introduce SCITO-seq, a cost-effective and ultra-high-throughput workflow for dsc-seq.
Enable combinatorial indexing of DNA-barcoded antibodies for large-scale single-cell protein analysis.
Develop a flexible platform for multimodal single-cell profiling.

Main Methods:

Utilized splint oligonucleotides (oligos) for combinatorial indexing in dsc-seq.
Encoded sample barcodes into splint oligos for multiplexed analysis.
Developed modified splint oligo designs for commercial DNA-barcoded antibody compatibility and multimodal profiling.

Main Results:

SCITO-seq processed over 10^5 cells per reaction using commercial microfluidics.
Multiplexed SCITO-seq provided reproducible cellular composition and surface protein expression estimates comparable to mass cytometry.
Demonstrated simultaneous transcriptome and surface protein profiling from the same cell.

Conclusions:

SCITO-seq offers a flexible and ultra-high-throughput platform for sequencing-based single-cell protein profiling.
The workflow significantly reduces the cost per cell for dsc-seq applications.
SCITO-seq enables large-scale pooled screens and clinical applications previously limited by cost.