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E-GEOD-27063 - affy_rnai_cadpoplars: Transcriptome analysis of RNAi-CAD transgenic poplars

Status
Released on 29 September 2011, last updated on 12 October 2011
Organism
Populus tremula x Populus alba
Samples (4)
Array (1)
Protocols (13)
Description
affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done. 4 arrays - poplar; normal vs rnai mutant comparaison
Experiment type
transcription profiling by array 
Contacts
stephanie huguet <huguet@evry.inra.fr>, Annabelle Dejardin, Marie-Laure Martin-Magniette, Sandrine Balzergue, Stephanie Huguet
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-27063.idf.txt
Sample and data relationshipE-GEOD-27063.sdrf.txt
Raw data (1)E-GEOD-27063.raw.1.zip
Processed data (1)E-GEOD-27063.processed.1.zip
Array designA-AFFY-131.adf.txt
R ExpressionSetE-GEOD-27063.eSet.r
Links