Transcriptomics

Dataset Information

4

Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens


ABSTRACT: Bryophytes are the most basal of the extant land plants. A major feature of these plants is the biphasic alteration of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. To analyse the differences in the transcriptome of the early gametophyte (protonema) and early and mid-sporophyte phases of the moss Physcomitrella patens, microarray gene expression profiles were performed using dissected sporophyte tissue. Through further analysis the early and mid-sporophyte phases were compared. RNA isolated from the Gametophytic protonemal tissue was hybridised to six microarrays. Each microarray was hybridised with RNA from a separate biological replicate. Three of these microarrays were co-hybridised with RNA isolated from early sporophytes. With the third gametophyte biological replicate and early sporophyte replicate a dye swap was carried out. The remaining three microarrays hybridised with RNA from the gametophytes were co-hybridised with RNA from mid-sporophytic tissue. A dye swap was carried out on the sixth gametophyte replicate and third mid-sporophyte replicate.To meet the quality requirements for the microarray experiment, at least 400 sporophytes were used per extraction. Three or four RNA extracts were then pooled for further precipitation to maximise purity and concentration. Up to 1600 sporophytes were harvested to prepare sufficient RNA for each microarray replicate. In bioinformatic analysis the channels were split into individual channels and the early and mid-sporophyte were compared.

ORGANISM(S): Physcomitrella patens  

SUBMITTER: Andrew J Fleming   Caspar Chater  Simon Wallace  Martin-Timothy O'Donoghue  David J Beerling  Julie E Gray 

PROVIDER: E-GEOD-32928 | ArrayExpress | 2013-07-29

SECONDARY ACCESSION(S): GSE32928PRJNA146495

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens.

O'Donoghue Martin-Timothy MT   Chater Caspar C   Wallace Simon S   Gray Julie E JE   Beerling David J DJ   Fleming Andrew J AJ  

Journal of experimental botany 20130725 12


Bryophytes, the most basal of the extant land plants, diverged at least 450 million years ago. A major feature of these plants is the biphasic alternation of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. These dramatic differences in form and function occur in a constant genetic background, raising the question of whether the switch from gametophyte-to-sporophyte development reflects major changes in the spectrum of genes being expressed or alternativel  ...[more]

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