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Series GSE29171 Query DataSets for GSE29171
Status Public on Feb 27, 2012
Title Comparative study of transcriptomes from four Trichoderma strains gene expression in early interaction with tomato plants
Platform organisms Trichoderma virens; Trichoderma reesei
Sample organisms Trichoderma harzianum; Trichoderma virens; Trichoderma hamatum; Trichoderma reesei
Experiment type Expression profiling by array
Summary A self-designed Trichoderma high density oligonuclotide (HDO) microarray (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 14,081 EST-derived transcripts (Trichochip-1) and the genomes of T. reesei (9,129 genes) and T. virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum), under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (VizcaĆ­no et al., 2006). This HDO microarray was used to analyze Trichoderma spp. transcriptomes after 20 h incubation in the presence of tomato plants.
The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032).
 
Overall design Eight samples were analyzed as follows: Strain T. parareesei T6 grown in the presence or not of tomato plants, strain T. hamatum T7 grown in the presence or not of tomato plants, strain T. harzianum T34 grown in the presence or not of tomato plants and strain T. virens T87 grown in the presence or not of tomato plants. Three replicates for each samples were performed.
 
Contributor(s) Rubio B, Hermosa R, Monte E
Citation(s) 22075029, 24413597
Submission date May 10, 2011
Last update date Sep 15, 2014
Contact name Enrique Monte
E-mail(s) emv@usal.es
Phone 34923294500 (5119)
Organization name University of Salamanca
Department Spanish-Portuguese Centre for Agricultural Research
Lab 2
Street address Rio Duero
City Salamanca
State/province Salamanca
ZIP/Postal code 37185
Country Spain
 
Platforms (1)
GPL13511 Nimblegen T.reesei & T.virens Trichochip-1 393K v1.0
Samples (24)
GSM721868 34 (43809802)
GSM721869 34 (43810202)
GSM721870 34 (43821602)
Relations
BioProject PRJNA140097

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
GSE29171_RAW.tar 314.0 Mb (http)(custom) TAR (of CALLS, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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