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  The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

Perroud, P.-F., Haas, F. B., Hiss, M., Ullrich, K. K., Alboresi, A., Amirebrahimi, M., et al. (2018). The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data. The Plant Journal, 95(1), 168-182. doi:10.1111/tpj.13940.

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 Creators:
Perroud, Pierre-Francßois, Author
Haas, Fabian B., Author
Hiss, Manuel, Author
Ullrich, Kristian K.1, Author              
Alboresi, Alessandro, Author
Amirebrahimi, Mojgan, Author
Barry, Kerrie, Author
Bassi, Roberto, Author
Bonhomme, Sandrine, Author
Chen, Haodong, Author
Coates, Juliet C., Author
Fujita, Tomomichi, Author
Guyon-Debast, Anouchka, Author
Lang, Daniel, Author
Lin, Junyan, Author
Lipzen, Anna, Author
Nogué, Fabien, Author
Oliver, Melvin J., Author
de Léon, Ines Ponce, Author
Quatrano, Ralph S., Author
Rameau, Catherine, AuthorReiss, Bernd, AuthorReski, Ralf, AuthorRicca, Mariana, AuthorSaidi, Younousse, AuthorSun, Ning, AuthorSzövenyi, Peter, AuthorSreedasyam, Avinash, AuthorGrimwood, Jane, AuthorStacey, Gary, AuthorSchmutz, Jeremy, AuthorRensing, and Stefan A., Author more..
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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Free keywords: Laboratories; Plants (botany); Quality control; RNA; Stresses, Developmental stage; differential expression; Differentially expressed gene; Growth conditions; High throughput; Physcomitrella patens; Physico-chemicals; Transcriptome analysis, Gene expression
 Abstract: High-throughput RNA sequencing (RNA-seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages – protonema, gametophore and sporophyte – allowed us to define both general transcriptional patterns and stage-specific transcripts. As an example of variation of physico-chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter-laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories. © 2018 The Authors The Plant Journal © 2018 John Wiley Sons Ltd

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Language(s): eng - English
 Dates: 2018-04-022017-11-292018-04-052018-04-222018
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1111/tpj.13940
BibTex Citekey: Perroud2018168
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Title: The Plant Journal
  Other : Plant J.
Source Genre: Journal
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Publ. Info: Oxford : Blackwell Science
Pages: - Volume / Issue: 95 (1) Sequence Number: - Start / End Page: 168 - 182 Identifier: ISSN: 0960-7412
CoNE: https://pure.mpg.de/cone/journals/resource/954925579095_1