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Institut für Pflanzengenetik
Logo Leibniz Universität Hannover
Institut für Pflanzengenetik
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Microarrays

Please enquire for the current version of our plant 70mer oligonucleotide microarray hybridization manual that includes protocols for probe preparation, target labeling, hybridization, and data acquisition.

Medicago truncatula Mt16kOLI1 70mer oligonucleotide microarray

Based on a joint initiative with the Samuel Roberts Noble Foundation, we purchased a set of 16.086 70mer oligonucleotides representing all tentative consensus sequences (TCs) from the DFCI Medicago truncatula Gene Index 5 (Medicago Genome Oligo Set Version 1.0, Operon). This set of 5' C6 amino-linker modified oligonucleotides is supplemented with different oligonucleotides that serve for control purposes and allow a detection of common transgenes. Mt16kOLI1 microarrays were printed with 2 replicate spots per microarray. Groups interested in obtaining Mt16kOLI1 microarrays in the frame of a research cooperation should enquire for conditions of use. Different documentations are available on request:

  • ImaGene GeneID-file for Mt16kOLI1 microarrays.
  • ImaGene grid-file for Mt16kOLI1 microarrays.
  • GenePix GeneID-file for Mt16kOLI1 microarrays.
  • ArrayExpress ADF-file for Mt16kOLI1 microarrays.
  • Annotation update for all probes of Mt16kOLI1 microarrays.

Medicago truncatula Mt16kOLI1Plus 70mer oligonucleotide microarray

Using a collection of 384 70mer oligonucleotides (Medicago Genome Oligo Set Version 1.0 Upgrade, Operon) primarily targeted against transcription factors and other regulators (selected by J. Gouzy and P. Gamas, LIPM, INRA Toulouse), Mt16kOLI1 microarrays were upgraded to Mt16kOLI1Plus versions in the frame of the EU FP6 Integrated Project GRAIN LEGUMES. Different documentations are available on request:

  • ImaGene GeneID-file for Mt16kOLI1Plus microarrays.
  • ImaGene grid-file for Mt16kOLI1Plus microarrays.
  • GenePix Gene-ID file for Mt16kOLI1Plus microarrays.
  • ArrayExpress ADF-file for Mt16kOLI1Plus microarrays.
  • Annotation update for all probes of Mt16kOLI1Plus microarrays.

Pisum sativum Ps6kOLI1 70mer oligonucleotide microarray

Based on 11930 Pisum sativum ESTs supplied by Hans Weber and Ruslana Radchuk (IPK Gatersleben; 8412 ESTs from cotyledons and seed coats), Aymeric Duclert (INRA Evry and Genoplante; 2816 ESTs from stipules, epicotyls, leaves, stems and seeds) and Julie Hofer (JIC Norwich; 702 ESTs from lateral and apical shoot tips before and during flowering), EST clustering was performed. The 5220 EST-clusters obtained formed the basis for a Pisum sativum 70mer oligonucleotide microarray (Pisum_sativum Genome Oligo Set Version 1.0, Operon). This microarray also contains positive control oligos detecting different pea marker genes, negative control oligos to assess microarray background level, several specificity and labeling control oligos, as well as different oligos that detect commonly used transgenes. The Ps6kOLI1 microarray was produced in the frame of the EU FP6 Integrated Project GRAIN LEGUMES. Different documentations are available on request:

  • ImaGene GeneID-file for Ps6kOLI1 microarrays.
  • ImaGene grid-file for Ps6kOLI1 microarrays.
  • GenePix GeneID-file for Ps6kOLI1 microarrays.
  • ArrayExpress ADF-file for Ps6kOLI1 microarrays.
  • Annotation update for all probes of Ps6kOLI1 microarrays.

Pt2.4kOLI1 70mer oligonucleotide microarray

Based on 2350 Populus tremula EST-clusters (Uwe Nehls, Universität Tübingen), Pt2.4kOLI1 70mer oligonucleotide microarrays were constructed that represent the Populus tremula ectomycorrhizal root transcriptome. These microarrays are produced in the frame of the DFG Priority Program MolMyk. Different documentations are available on request:

  • ImaGene GeneID-file for Pt2.4kOLI1 microarrays.
  • ImaGene grid-file for Pt2.4kOLI1 microarrays.
  • ArrayExpress ADF-file for Pt2.4kOLI1 microarrays.

Mt6k-RIT cDNA macro- and microarray

Eight European labs participated in a joint expression profiling approach in the European Union project MEDICAGO. This project relied on a collection of ~25.000 ESTs derived from root nodules, mycorrhizal roots and nitrogen-starved roots, provided by the CNRS and INRA labs in Toulouse and Dijon, and being clustered into ~6.300 different groups. After re-arraying, a set of 6.048 viable cluster-representative ESTs was identified and enriched with a limited number of ESTs from roots interacting with the pathogenic fungus Aphanomyces euteiches and by ESTs from a suppression-subtractive hybridization (SSH) library from mycorrhizal roots. From a set of 5.646 PCR-products, Mt6k-RIT macroarrays (nylon membranes) and Mt6kRIT microarrays (glass slides) were gridded/printed. Mt6k-RIT macro- and microarrays were used within the European Union project MEDICAGO, the INRA ATS network and the DFG Priority Program MolMyk.

Mt8k cDNA microarray

The collection of PCR products used for Mt6k-RIT construction was extended by 1.776 PCR-products representing M. truncatula genes expressed in flowers, seeds and pods. These genes were identified in the course of an EST sequencing project covering different stages of flower and pod development. Together, these two sets of PCR-products were arrayed on Mt8k microarrays that were used in the European Union project MEDICAGO and the DFG Priority Program MolMyk.