An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser capture microdissection coupled to RNA-seq

We developed an approach based upon RNA-seq coupled to laser micro-dissection to analyze gene expression in indeterminate nodules, where spatial zonation corresponds to successive developmental stages.
We thus obtained data simultaneously for the plant and the bacteria, with a comparison between five nodule regions, from the apical meristem to the nitrogen fixation zone.
RNA-seq data were also produced from whole (non laser-dissected) nitrogen-starved root systems and mature nodules, allowing for differential analyses of gene expression between roots and nodules.
Whole organ analyses were carried out independently on polyA+ RNAs and on RNA populations enriched in plant and bacterial mRNAs by oligo-depetion of rRNAs (termed ribominus RNA).

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Transcript variation in M. truncatula and S. meliloti pathways
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