Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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. We analyzed 2 sets of arrays (8 arrays each): one from growth under silicon replete and another one from growth under silicon deplete conditions.

ORGANISM(S): Thalassiosira pseudonana CCMP1335

SUBMITTER: Michael Sussman

PROVIDER: E-GEOD-9661 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses.

Mock Thomas T Samanta Manoj Pratim MP Iverson Vaughn V Berthiaume Chris C Robison Matthew M Holtermann Karie K Durkin Colleen C Bondurant Sandra Splinter SS Richmond Kathryn K Rodesch Matthew M Kallas Toivo T Huttlin Edward L EL Cerrina Francesco F Sussman Michael R MR Armbrust E Virginia EV

Proceedings of the National Academy of Sciences of the United States of America 20080122 5

Formation of complex inorganic structures is widespread in nature. Diatoms create intricately patterned cell walls of inorganic silicon that are a biomimetic model for design and generation of three-dimensional silica nanostructures. To date, only relatively simple silica structures can be generated in vitro through manipulation of known diatom phosphoproteins (silaffins) and long-chain polyamines. Here, we report the use of genome-wide transcriptome analyses of the marine diatom Thalassiosira p ...[more]

PMID: 18212125

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Dataset Information

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

Publications

Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses.

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