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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 microarray-based...

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Updated: Jun 16, 2026

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.

Andrew H Beck¹, Ziming Weng, Daniela M Witten

¹Department of Pathology, Stanford University Medical Center, Stanford, California, United States of America.

|January 26, 2010

Summary

This summary is machine-generated.

3SEQ gene expression profiling effectively analyzes formalin-fixed paraffin-embedded tissues, overcoming microarray limitations. This novel method enables comprehensive gene expression analysis from archival tumor samples for cancer research.

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Published on: October 10, 2017

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

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

Published on: April 11, 2016

Area of Science:

Oncology
Genomics
Molecular Biology

Background:

Gene expression microarrays are standard for genome-wide profiling but perform poorly on formalin-fixed paraffin-embedded tissue (FFPET).
This limitation restricts gene expression profiling of the extensive archives of tumor samples.

Purpose of the Study:

To develop and validate a novel method, 3'-end sequencing for expression quantification (3SEQ), for gene expression profiling from FFPET.
To compare the efficacy of 3SEQ with microarrays using both frozen and FFPET samples.

Main Methods:

Gene expression profiling was performed using 3SEQ and microarrays on frozen and FFPET samples from two soft tissue tumors (desmoid type fibromatosis and solitary fibrous tumor).
Differential gene expression analysis and functional gene set enrichment analysis were conducted.

Main Results:

3SEQ identified significantly more differentially expressed genes (approx. 9.6K in frozen, 8.1K in FFPET) compared to microarrays (approx. 4.64K in frozen, 69 in FFPET).
3SEQ analysis revealed known and suggested novel oncogenic pathways in the tumors.
3SEQ demonstrated high performance on FFPET, comparable to frozen tissue.

Conclusions:

3SEQ is a highly effective technique for gene expression profiling from archival FFPET.
This method overcomes the limitations of microarrays and can advance translational cancer research by enabling analysis of valuable tissue archives.