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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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Related Experiment Video

Updated: Sep 20, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Whole-Transcriptome Profiling on Small FFPE Samples: Which Sequencing Kit Should Be Used?

Marc Hilmi¹, Lucile Armenoult², Mira Ayadi²

¹Molecular Oncology, PSL Research University, CNRS, UMR 144, Institut Curie, 75005 Paris, France.

Current Issues in Molecular Biology

|June 9, 2022

Summary

This summary is machine-generated.

This study compares RNA sequencing kits for formalin-fixed paraffin-embedded (FFPE) cancer samples. The Smarter Pico V3 ribodepletion method is the most reliable and reproducible for low-quantity FFPE RNA.

Keywords:

RNA sequencing formalin-fixed paraffin-embedded samples library preparation

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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Last Updated: Sep 20, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

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Published on: April 11, 2016

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Area of Science:

Molecular Biology
Genomics
Oncology

Background:

RNA sequencing (RNA-Seq) holds significant clinical potential in oncology.
Formalin-fixed paraffin-embedded (FFPE) samples are abundant but challenging for RNA-Seq due to limited RNA quantity.
A comparative analysis of FFPE-compatible RNA-Seq kits, especially for low-input samples, is lacking.

Purpose of the Study:

To evaluate and compare the performance of five FFPE-compatible RNA-Seq kits.
To identify the most reliable, cost-effective, and relevant RNA-Seq approach for low-quantity FFPE samples.
To assess gene expression correlation and reproducibility across different kits and sample types.

Main Methods:

Five FFPE-compatible RNA-Seq kits (3′ capture, exome-capture, ribodepletion) were tested using 8 ng to 400 ng of FFPE-derived RNA.
Performance was compared against Nanostring on FFPE samples and a reference PolyA (Truseq) approach on flash-frozen samples.
Gene expression correlations and reproducibility were analyzed.

Main Results:

The Smarter Pico V3 ribodepletion approach demonstrated the highest systematic comparability to Nanostring and Truseq (p < 0.001).
Smarter Pico V3 exhibited high reproducibility across experiments.
Compared to exome-capture and 3′ kits, the Smarter approach showed greater comparability with the Truseq reference.

Conclusions:

The Smarter Pico V3 is recommended as the most robust RNA-Seq technique for analyzing small FFPE samples.
The 3′ Lexogen kit offers a favorable quality-price ratio for samples with less restricted RNA quantities.