E-MEXP-877 - Transcription profiling of Arabidopsis or Thlaspi caerulescens roots exposed to deficient, sufficient or excess zinc

Status
Released on 10 October 2006, last updated on 2 May 2014
Organism
Arabidopsis thaliana, Thlaspi caerulescens
Samples (12)
Array (1)
Protocols (7)
Description
A common reference model was used to design the microarray experiment, in which cDNA from T. caerulescens roots exposed to 100 uM (sufficient) zinc was used as the common reference. Every slide was always hybridized with the common reference sample and with a sample from one of the treatments (Arabidopsis or T. caerulescens exposed to deficient, sufficient or excess zinc). The common reference was labeled with the fluorescent dye Cyanine 3 (Cy3) and the treatment samples were labeled with Cyanine 5 (Cy5). As a quality control step we performed a dye-swap hybridization for one sample (from T. caerulescens roots exposed to sufficient zinc).
Experiment types
transcription profiling by array, comparative genome hybridization, growth condition, reference
Contacts
Judith E van de Mortel <judith.vandemortel@wur.nl>, Emiel Ver Loren van Themaat, Henk Schat, Jeroen Kwekkeboom, Laia Almar Villanueva, Maarten Koornneef, Mark Aarts, Perry D Moerland, Sean Coughlan
Citation
Large Expression Differences in Genes for Iron and Zinc Homeostasis, Stress Response, and Lignin Biosynthesis Distinguish Roots of Arabidopsis thaliana and the Related Metal Hyperaccumulator Thlaspi caerulescens. van de Mortel, Judith E.; Almar Villanueva, Laia; Schat, Henk; Kwekkeboom, Jeroen; Coughlan, Sean; Moerland, Perry D.; Ver Loren van Themaat, Emiel; Koornneef, Maarten; Aarts, Mark G.M.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MEXP-877.idf.txt
Sample and data relationshipE-MEXP-877.sdrf.txt
Raw data (1)E-MEXP-877.raw.1.zip
Array designA-AGIL-12.adf.txt
R ExpressionSetE-MEXP-877.eSet.r
Links