Gene Expression
There are several publicly available resources for gene expression.
The Affymetrix GeneChip® Medicago Genome Array was designed in 2005 using a combination of annotated BAC sequwnces EST-derived TCs and singletons from Medicago species to monitor gene expression in Medicago truncatula, Medicago sativa as well as the symbiotic organism Sinorhizobium meliloti. The tables/database contains all probes and their corresponding targets, gene IDs are linked to the TIGR Medicago Gene Index TCs/ESTs, IMGAG genes and TIGR 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 Mt3.5v5 Annotation 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.
RNA-seq data
There is now considerable RNA-seq data documenting gene expression in a variety of M. truncatula tissues and states. 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.
TIGR Plant Transcript Assemblies
All publicly available M. truncatula ESTs as well as transcripts from GenBank was assembled into contigs and the annotated assemblies made public. These assemblies are now outdated and have been taken off-line, but can be retrieved from the Medicago Transcript Assemblies page.
Medicago truncatula Gene Index
The Medicago truncatula Gene Index (MtGI) is now hosted at the Dana Faber Cancer Center.
Operon 16K oligonucleotides array
This was developed in collaboration with Operon, based upon MtGI 5.0. The probe set was later mapped to MtGI Release 8.0 (Threshold 98.5% ID, 90% coverage). SLIM GO annotation was performed by mapping to the TAIR Arabidopsis assignments (threshold e-10, from a database size of 119546). Over 13,000 probes/TCs were assigned a SLIM GO annotation.
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