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Series GSE9661 Query DataSets for GSE9661
Status Public on Jan 09, 2008
Title Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.
Organism Thalassiosira pseudonana CCMP1335
Experiment type Expression profiling by genome tiling array
Summary 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
Overall design We analyzed 2 sets of arrays (8 arrays each): one from growth under silicon replete and another one from growth under silicon deplete conditions.
Contributor(s) Mock T, Samanta MP, Iverson V, Berthiaume C, Robison M, Rodesch M, Holtermann K, Durkin C, SplinterBonDurant S, Richmond K, Kallas T, Huttlin EL, Cerrina F, Sussman MR, Armbrust EV
Citation(s) 18212125
Submission date Nov 21, 2007
Last update date Mar 19, 2012
Contact name E. Virginia Armbrust
Organization name University of Washington
Department Oceanography
Lab Armbrust Lab
Street address Ben Hall IRB, 616 NE Northlake Pl, Room 306
City Seattle
State/province WA
ZIP/Postal code 98105
Country USA
Platforms (1)
GPL6176 Thalassiosira pseudonana NimbleGen 36mer oligo tiling array
Samples (2)
GSM244159 T.pseudonana1335_tiling-array_Control
GSM244160 T.pseudonana1335_tiling-array_Si
This SubSeries is part of SuperSeries:
GSE9697 Gene profiling of Thalassiosira pseudonana under various growth conditions
BioProject PRJNA105087

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9661_RAW.tar 106.4 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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