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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 31, 2025

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing.

Zhuo-Xing Shi¹, Zhi-Chao Chen², Jia-Yong Zhong¹

¹State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.

Nature Communications

|May 6, 2023

Summary

This summary is machine-generated.

HIT-scISOseq enhances single-cell RNA isoform sequencing by removing artifacts and concatenating cDNAs. This high-throughput method provides millions of accurate long-reads, accelerating single-cell transcriptomics research.

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Last Updated: Jul 31, 2025

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

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

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:

Molecular Biology
Genomics
Bioinformatics

Background:

Single-cell RNA isoform sequencing (scISO-Seq) offers insights into cellular RNA splicing.
Existing scISO-Seq methods face limitations in read throughput, hindering comprehensive analysis.

Purpose of the Study:

To develop a high-throughput and high-accuracy method for single-cell RNA isoform sequencing.
To introduce a computational tool for accurate demultiplexing of concatenated cDNA reads.

Main Methods:

HIT-scISOseq: A method involving artifact cDNA removal and cDNA concatenation for PacBio circular consensus sequencing (CCS).
scISA-Tools: A computational tool for demultiplexing concatenated reads with high accuracy (>99.99%).
Application to 3375 corneal limbus cells to analyze transcriptomes.

Main Results:

HIT-scISOseq generates over 10 million high-accuracy long-reads per PacBio Sequel II SMRT Cell 8M.
scISA-Tools achieves >99.99% accuracy and specificity in demultiplexing.
Characterization of transcriptomes in 3375 corneal limbus cells, revealing cell-type-specific isoform expression.

Conclusions:

HIT-scISOseq is a high-throughput, high-accuracy, and accessible method for long-read single-cell transcriptomics.
The method and associated tools significantly advance the field of single-cell RNA isoform analysis.
Enables deeper understanding of cellular heterogeneity and gene expression regulation.