ResearchSectionsPlant Genomics
Microarrays and GeneChips

Microarrays and GeneChips

Subsequent generations of array-based expression profiling tools were constructed and/or used to identify host genes differentially regulated during the initiation and development of beneficial plant-microbe interactions, in particular the arbuscular mycorrhiza symbiosis.

 

GeneChip® Medicago Genome Array

The GeneChip® Medicago Genome Array (ThermoFisher Scientific) was designed in 2005 and allows to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiont Sinorhizobium meliloti. The GeneChip® contains more than 61200 probe sets: 32167 M. truncatula transcript-based and chloroplast genome-based probe sets, 18733 M. truncatula genome-based  probe sets, 1896 M. sativa transcript-based probe sets, and 8305 S. meliloti genome-based probe sets. Based on comparisons to the Medicago truncatula genome release 4.0, ~70% of the Medicago truncatula genome are covered by GeneChip® Medicago Genome Arrays.

GeneChip® Medicago Transcriptome Assay

The GeneChip® Medicago Transcriptome Assay (ThermoFisher Scientific) is based on the Medicago truncatula genome release 4.0 and, apart from allowing genome-wide expression profiling, can be used for the detection of alternative splicing events.

Medicago truncatula Mt16kOLI1 70mer oligonucleotide microarrays

In a joint initiative with the Samuel Roberts Noble Foundation, we used 16086 70mer oligonucleotides representing Medicago truncatula transcript cluster sequences (Medicago Genome Oligo Set 1.0) to develop Mt16kOLI microarrays.

Medicago truncatula Mt16kOLI1Plus 70mer oligonucleotide microarrays

Using 384 70mer oligonucleotides primarily targeted at transcription factor genes, Mt16kOLI1 microarrays were upgraded to Mt16kOLI1Plus in frame of the EU Project GRAIN LEGUMES.

Pisum sativum Ps6kOLI1 70mer oligonucleotide microarrays

Pisum sativum 70mer oligonucleotide (Pisum sativum Genome Oligo Set 1.0) microarrays (Ps6kOLI1), representing 5220 transcript cluster sequences, were developed in the frame of the EU Project GRAIN LEGUMES.

Medicago truncatula Mt6kRIT cDNA macro- and microarrays

In the EU Project MEDICAGO, ~25000 transcript sequences from root nodules, mycorrhizal roots and nitrogen-starved roots were clustered into ~6300 different groups. From a set of 5646 PCR products, Mt6kRIT macro- and microarrays were printed.

Medicago truncatula Mt8k cDNA macro- and microarrays

To develop Mt8k arrays, the set of PCR products used for Mt6kRIT arrays was extended by 1776 PCR products representing M. truncatula genes expressed in flowers, seeds and pods.