An atlas of gene expression from seed to seed through barley development

Arnis Druka, Gary Muehlbauer, Ilze Druka, Rico Caldo, Ute Baumann, Nils Rostoks, Andreas Schreiber, Roger Wise, Timothy Close, Andris Kleinhofs, Andreas Graner, Alan Schulman, Peter Langridge, Kazuhiro Sato, Patrick Hayes, Jim McNicol, David Marshall, Robbie Waugh

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105 Citations (Scopus)

Abstract

Assaying relative and absolute levels of gene expression in a diverse series of tissues is a central step in the process of characterizing gene function and a necessary component of almost all publications describing individual genes or gene family members. However, throughout the literature, such studies lack consistency in genotype, tissues analyzed, and growth conditions applied, and, as a result, the body of information that is currently assembled is fragmented and difficult to compare between different studies. The development of a comprehensive platform for assaying gene expression that is available to the entire research community provides a major opportunity to assess whole biological systems in a single experiment. It also integrates detailed knowledge and information on individual genes into a unified framework that provides both context and resource to explore their contributions in a broader biological system. We have established a data set that describes the expression of 21,439 barley genes in 15 tissues sampled throughout the development of the barley cv. Morex grown under highly controlled conditions. Rather than attempting to address a specific biological question, our experiment was designed to provide a reference gene expression data set for barley researchers; a gene expression atlas and a comparative data set for those investigating genes or regulatory networks in other plant species. In this paper we describe the tissues sampled and their transcriptomes, and provide summary information on genes that are either specifically expressed in certain tissues or show correlated expression patterns across all 15 tissue samples. Using specific examples and an online tutorial, we describe how the data set can be interrogated for patterns and levels of barley gene expression and how the resulting information can be used to generate and/or test specific biological hypotheses.
Original languageEnglish
Pages (from-to)202-211
JournalFunctional and Integrative Genomics
Volume6
Issue number3
DOIs
Publication statusPrint publication - Mar 2006
Externally publishedYes

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barley
gene expression
seeds
genes
transcriptome
tissues
researchers
genotype
testing
sampling

Cite this

Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., ... Waugh, R. (2006). An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics, 6(3), 202-211. https://doi.org/10.1007/s10142-006-0025-4
Druka, Arnis ; Muehlbauer, Gary ; Druka, Ilze ; Caldo, Rico ; Baumann, Ute ; Rostoks, Nils ; Schreiber, Andreas ; Wise, Roger ; Close, Timothy ; Kleinhofs, Andris ; Graner, Andreas ; Schulman, Alan ; Langridge, Peter ; Sato, Kazuhiro ; Hayes, Patrick ; McNicol, Jim ; Marshall, David ; Waugh, Robbie. / An atlas of gene expression from seed to seed through barley development. In: Functional and Integrative Genomics. 2006 ; Vol. 6, No. 3. pp. 202-211.
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Druka, A, Muehlbauer, G, Druka, I, Caldo, R, Baumann, U, Rostoks, N, Schreiber, A, Wise, R, Close, T, Kleinhofs, A, Graner, A, Schulman, A, Langridge, P, Sato, K, Hayes, P, McNicol, J, Marshall, D & Waugh, R 2006, 'An atlas of gene expression from seed to seed through barley development', Functional and Integrative Genomics, vol. 6, no. 3, pp. 202-211. https://doi.org/10.1007/s10142-006-0025-4

An atlas of gene expression from seed to seed through barley development. / Druka, Arnis; Muehlbauer, Gary; Druka, Ilze; Caldo, Rico; Baumann, Ute; Rostoks, Nils; Schreiber, Andreas; Wise, Roger; Close, Timothy; Kleinhofs, Andris; Graner, Andreas; Schulman, Alan; Langridge, Peter; Sato, Kazuhiro; Hayes, Patrick; McNicol, Jim; Marshall, David; Waugh, Robbie.

In: Functional and Integrative Genomics, Vol. 6, No. 3, 03.2006, p. 202-211.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Muehlbauer, Gary

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AU - Caldo, Rico

AU - Baumann, Ute

AU - Rostoks, Nils

AU - Schreiber, Andreas

AU - Wise, Roger

AU - Close, Timothy

AU - Kleinhofs, Andris

AU - Graner, Andreas

AU - Schulman, Alan

AU - Langridge, Peter

AU - Sato, Kazuhiro

AU - Hayes, Patrick

AU - McNicol, Jim

AU - Marshall, David

AU - Waugh, Robbie

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