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Browse PoplarPLEX Experiment Data

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affy_rnai_cadpoplars: Transcriptome analysis of RNAi-CAD transgenic poplars
Stephanie Huguet, INRA, Department of URGV, Evry, France (huguet@evry.inra.fr)
Experiment design (4 hybridizations)
genetic line
•RNAi-CAD •control

This experiment has been imported by PLEXdb from NCBI GEO (GSE27063)

Series_summary:
affy_rnai_cadpoplar - affy_rnai_cadpoplars - Thi...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: affy_rnai_cadpoplars: Transcriptome analysis of RNAi-CAD transgenic poplars
Accession No: PT37
Microarray: Poplar61k
Visibility: public
Experiment Type:
Experiment Factor(s):
genetic line
•RNAi-CAD   •control
Quality Control: biological replicates
Treatment summary:
 genetic line  # replicates
 RNAi-CAD  2
 control  2
Total hybridizations: 4
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE27063)

Series_summary:
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.

Series_overall_design:
4 arrays - poplar; normal vs rnai mutant comparaison
Publication: none
Created: 2011-11-03 10:16:15
Last Update: 2011-11-03 13:26:26
Released: 2011-11-03
GEO Accession GSE27063
Submitter: PLEXdb Curator
Name: Stephanie Huguet
Institution: INRA, Department of URGV, Evry, France
Head of Laboratory: Claire Lurin
email(s):
Homepage:

 
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