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Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.

ABSTRACT: T. pseudonana tiling arrays were used to validate gene models and to predict new genes in the genome of this diatom. The tiling array data validated transcription of about 41% (4,653) of the 11,390 computationally predicted genes. An additional 1,132 transcripts were identified that did not correspond to modeled genes with few of these transcripts (<17%) predicted to encode proteins with homology (e-value < 10-05) to publicly available proteins. These newly identified transcripts have an average length of 1,549 bp, comparable to the average length of the computationally derived genes. Whole genome tiling arrays were conducted under silicon replete and deplete growth conditions to identify new genes involved in the synthesis of the diatom silica cell wall. Keywords: silicon, stress response, cell wall

ORGANISM(S): Thalassiosira pseudonana CCMP1335

PROVIDER: GSE9661 | GEO | 2008/01/09

SECONDARY ACCESSION(S): PRJNA105087

REPOSITORIES: GEO

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Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.

Project description:T. pseudonana tiling arrays were used to validate gene models and to predict new genes in the genome of this diatom. The tiling array data validated transcription of about 41% (4,653) of the 11,390 computationally predicted genes. An additional 1,132 transcripts were identified that did not correspond to modeled genes with few of these transcripts (<17%) predicted to encode proteins with homology (e-value < 10-05) to publicly available proteins. These newly identified transcripts have an average length of 1,549 bp, comparable to the average length of the computationally derived genes. Whole genome tiling arrays were conducted under silicon replete and deplete growth conditions to identify new genes involved in the synthesis of the diatom silica cell wall. We analyzed 2 sets of arrays (8 arrays each): one from growth under silicon replete and another one from growth under silicon deplete conditions.

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