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Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as co...

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Autores principales: Poeschl, Yvonne, Delker, Carolin, Trenner, Jana, Ullrich, Kristian Karsten, Quint, Marcel, Grosse, Ivo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832635/
https://www.ncbi.nlm.nih.gov/pubmed/24260119
http://dx.doi.org/10.1371/journal.pone.0078497
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author Poeschl, Yvonne
Delker, Carolin
Trenner, Jana
Ullrich, Kristian Karsten
Quint, Marcel
Grosse, Ivo
author_facet Poeschl, Yvonne
Delker, Carolin
Trenner, Jana
Ullrich, Kristian Karsten
Quint, Marcel
Grosse, Ivo
author_sort Poeschl, Yvonne
collection PubMed
description Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides a superior base for biological interpretation of the measured expression responses.
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spelling pubmed-38326352013-11-20 Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species Poeschl, Yvonne Delker, Carolin Trenner, Jana Ullrich, Kristian Karsten Quint, Marcel Grosse, Ivo PLoS One Research Article Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides a superior base for biological interpretation of the measured expression responses. Public Library of Science 2013-11-08 /pmc/articles/PMC3832635/ /pubmed/24260119 http://dx.doi.org/10.1371/journal.pone.0078497 Text en © 2013 Poeschl et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Poeschl, Yvonne
Delker, Carolin
Trenner, Jana
Ullrich, Kristian Karsten
Quint, Marcel
Grosse, Ivo
Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species
title Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species
title_full Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species
title_fullStr Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species
title_full_unstemmed Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species
title_short Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species
title_sort optimized probe masking for comparative transcriptomics of closely related species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832635/
https://www.ncbi.nlm.nih.gov/pubmed/24260119
http://dx.doi.org/10.1371/journal.pone.0078497
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