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SeedSeq: Off-Target Transcriptome Database

Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs). However, owing to a tolerance for mis...

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Detalles Bibliográficos
Autores principales: Das, Shaoli, Ghosal, Suman, Chakrabarti, Jayprokas, Kozak, Karol
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773410/
https://www.ncbi.nlm.nih.gov/pubmed/24069606
http://dx.doi.org/10.1155/2013/905429
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author Das, Shaoli
Ghosal, Suman
Chakrabarti, Jayprokas
Kozak, Karol
author_facet Das, Shaoli
Ghosal, Suman
Chakrabarti, Jayprokas
Kozak, Karol
author_sort Das, Shaoli
collection PubMed
description Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs). However, owing to a tolerance for mismatches and gaps in base-pairing with target transcripts, siRNAs could have up to hundreds of potential target sequences in a genome, and some small RNAs in mammalian systems have been shown to affect the levels of many messenger RNAs (off-targets) besides their intended target transcripts (on-targets). The reference sequence (RefSeq) collection aims to provide a comprehensive, integrated, nonredundant, well-annotated set of sequences, including mRNA transcripts. We performed a detailed off-target analysis of three most commonly used kinome siRNA libraries based on the latest RefSeq version. To simplify the access to off-target transcripts, we created a SeedSeq database, a new unique format to store off-target information.
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spelling pubmed-37734102013-09-25 SeedSeq: Off-Target Transcriptome Database Das, Shaoli Ghosal, Suman Chakrabarti, Jayprokas Kozak, Karol Biomed Res Int Research Article Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs). However, owing to a tolerance for mismatches and gaps in base-pairing with target transcripts, siRNAs could have up to hundreds of potential target sequences in a genome, and some small RNAs in mammalian systems have been shown to affect the levels of many messenger RNAs (off-targets) besides their intended target transcripts (on-targets). The reference sequence (RefSeq) collection aims to provide a comprehensive, integrated, nonredundant, well-annotated set of sequences, including mRNA transcripts. We performed a detailed off-target analysis of three most commonly used kinome siRNA libraries based on the latest RefSeq version. To simplify the access to off-target transcripts, we created a SeedSeq database, a new unique format to store off-target information. Hindawi Publishing Corporation 2013 2013-08-29 /pmc/articles/PMC3773410/ /pubmed/24069606 http://dx.doi.org/10.1155/2013/905429 Text en Copyright © 2013 Shaoli Das et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Das, Shaoli
Ghosal, Suman
Chakrabarti, Jayprokas
Kozak, Karol
SeedSeq: Off-Target Transcriptome Database
title SeedSeq: Off-Target Transcriptome Database
title_full SeedSeq: Off-Target Transcriptome Database
title_fullStr SeedSeq: Off-Target Transcriptome Database
title_full_unstemmed SeedSeq: Off-Target Transcriptome Database
title_short SeedSeq: Off-Target Transcriptome Database
title_sort seedseq: off-target transcriptome database
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773410/
https://www.ncbi.nlm.nih.gov/pubmed/24069606
http://dx.doi.org/10.1155/2013/905429
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