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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2013
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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. |
format | Online Article Text |
id | pubmed-3773410 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
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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