English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Optimized probe masking for comparative transcriptomics of closely related species

Poeschl, Y., Delker, C., Trenner, J., Ullrich, K. K., Quint, M., & Grosse, I. (2013). Optimized probe masking for comparative transcriptomics of closely related species. PLoS One, 8: e78497. doi:10.1371/journal.pone.0078497.

Item is

Files

show Files
hide Files
:
journal.pone.0078497&type=printable (Publisher version), 458KB
Name:
journal.pone.0078497&type=printable
Description:
-
OA-Status:
Visibility:
Public
MIME-Type / Checksum:
application/pdf / [MD5]
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Locators

show
hide
Description:
-
OA-Status:

Creators

show
hide
 Creators:
Poeschl, Y., Author
Delker, C., Author
Trenner, J., Author
Ullrich, K. K.1, Author           
Quint, M., Author
Grosse, I., Author
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

Content

show
hide
Free keywords: Arabidopsis/*physiology, DNA Probes/*chemistry/genetics, Gene Expression Profiling/*methods, Gene Expression Regulation, Plant/*physiology, Oligonucleotide Array Sequence Analysis/instrumentation/*methods, Species Specificity
 Abstract: 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.

Details

show
hide
Language(s): eng - English
 Dates: 2013-07-122013-09-132013-11-082013
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1371/journal.pone.0078497
BibTex Citekey: poeschl_optimized_2013
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: PLoS One
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: San Francisco, CA : Public Library of Science
Pages: 9 Seiten Volume / Issue: 8 Sequence Number: e78497 Start / End Page: - Identifier: ISSN: 1932-6203
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000277850