SSP GENE ATLAS DATABASE

The Gene Expression Atlas in Medicago truncatula is database that hosts a rich RNA-seq data from diverse biological conditions, such as macronutrient deficiencies, nodule development, salt stress, symbiotic interactions and different plant tissues (root, leaf, leaf bud, pod, flower, petiole, and bare stalk) of 423 samples from 129 conditions and 12 experiments. The SSP gene Atlas allows you to query for the expression levels of your gene(s)/transcript(s) of interest, and also analyze the expression or co-expression and visualize the results by line or bar graphs. The user has the option to download the relevant data and results by choosing the output format (table or graphs). The SSP Atlas provides a complete and an update transcriptomic profiles in M. truncatula with different analysis tools.

Summary

In total we have 70,094 genes and 4,425 SSP candidate genes from Mt3.5v5 and Mt4.0v1 genome assemblies, and also new genes were identified.
Experiment Samples Source
Macronutrient Deficiencies 1 24 Noble Research Institute, LLC
Macronutrient Deficiencies 2 6 Noble Research Institute, LLC
Nodule Development 1 7 Noble Research Institute, LLC
Nodule Development 2 12 Public available data from LIPM-INRA-CNRS
Nodule Development 3 36 Public available data from UCDAVIS
Salt Stress 8 Noble Research Institute, LLC
Symbiotic Interactions 1 3 Public available data from LIPM-INRA-CNRS
Symbiotic Interactions 2 4 Public available data from Garcia et al. 2017
Symbiotic Interactions 3 4 Public available data from Jardinaud et al. 2016
Symbiotic Interactions 4 12 Public available data from Luginbuehl et al 2017
Symbiotic Interactions 5 12 Public available data from Zeijl et al 2015
Plant Tissues 9 Noble Research Institute, LLC
The SSP Gene Expression Atlas will be available soon here. For any questions and comments about the SSP project, please contact the principal investigator of the project - Dr. Wolf Scheible (wrscheible@noble.org) or the Co-PI - Dr. Patrick Zhao (pzhao@noble.org) from Noble Research Institute. For questions and suggestions regarding the Web Server, please contact site administrator.