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Related Experiment Video

Updated: May 7, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

SeedSeq: off-target transcriptome database.

Shaoli Das¹, Suman Ghosal, Jayprokas Chakrabarti

¹Indian Association for the Cultivation of Science, Kolkata, West Bengal 700032, India.

Biomed Research International

|September 27, 2013

Summary

Short interfering RNAs (siRNAs) can target unintended sequences, impacting biological applications. A new SeedSeq database simplifies the analysis of these off-target effects in mammalian systems.

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3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Area of Science:

Molecular Biology
Bioinformatics

Background:

Accurate detection of unintended sequence interactions is vital for applications like high-content screening and RNA interference.
Short interfering RNAs (siRNAs) exhibit tolerance to mismatches, potentially leading to numerous off-target binding sites within a genome.
Mammalian small RNAs can affect multiple messenger RNA (mRNA) levels beyond their intended targets.

Purpose of the Study:

To conduct a comprehensive off-target analysis of commonly used kinome siRNA libraries.
To develop an accessible resource for identifying potential siRNA off-target transcripts.

Main Methods:

Utilized the latest RefSeq database for sequence annotation.
Performed detailed off-target analysis on three major kinome siRNA libraries.
Developed the SeedSeq database for storing and accessing off-target information.

Main Results:

Identified extensive potential off-target transcripts for the analyzed siRNA libraries.
Demonstrated the significant challenge of predicting siRNA specificity.
Established a novel database format for efficient off-target data management.

Conclusions:

Off-target effects are a significant consideration for siRNA-based applications.
The SeedSeq database provides a valuable tool for researchers to assess and mitigate siRNA off-target risks.
Improved prediction and management of off-target interactions are crucial for reliable biological research and therapeutic development.