Gene Expression

There are several publicly available resources for gene expression.

Microarrays

The Affymetrix GeneChip® Medicago Genome Array was designed in 2005 using a combination of annotated BAC sequences EST-derived TCs and single tons from Medicago species to monitor gene expression in Medicago truncatula, Medicago sativa as well as the symbiotic organism Sinorhizobium meliloti. The Noble Foundation, in collaboration with other groups in the community, have developed an extensive set of expression data that is accessible through the Medicago Gene Atlas (Benedito et al., 2008). A one to one mapping to the Mt4.0 annotation (transcripts) can be found on our ftp site.

The Agilent Expression Array contains oligonucleotides in a 4 x 44K format. The sequences of these probes and their mapping to the Mt3.5 annotation (located on the FTP site) can be downloaded from here. Mapping to the Mt4.0 annotation will be generated if requested.

RNA-seq data

There is now considerable RNA-seq data documenting gene expression in a variety of M. truncatula tissues and stages. Not all these data are publicly available at this time. However, views of gene expression in some tissues and developmental stages can be accessed through the Genome Browser.

Medicago transcript assemblies

The Medicago truncatula Gene Index (MtGI) is now hosted at the Dana Faber Cancer Center. A second source of transcript assemblies derived from Sanger sequencing can be found at PlantGDB.