EXPERIMENT OVERVIEW


RNA-seq data: 159 RNA-seq libraries were sequenced with Illumina NextSeq sequencing system (Noble Research Institute), and we also have 264 nodule development and symbiotic interactions libraries from publicly available data.

The data are from the following experiments:


Summary
Macronutrient Deficiencies 1 RNA-seq libraries were prepared from root and shoot tissues of plants grown under sulfur (S), potassium (K), nitrogen (N) and phosphorus depleted conditions. The response to persistent deficiency was tested by growing the plants for 3 weeks under full nutrition (FN) or under deficiency of N, P, K or S. Additional samples were collected from plants re-supplied with FN for 6 h following the nutrient-deficiency treatment.
Macronutrient Deficiencies 2 RNA-seq libraries were prepared from root and shoot tissues of plants grown under full nutrition, and with no nitrogen or phosphorus collected after 22 days of germination.
Nodule Development 1 RNA-seq libraries were obtained from root/nodule tissues at varying developmental stages of nodulation with Sinorhizobium meliloti. The stages were: pre-inoculated root; root at 4 dpi, harboring the initial nodule bump during initiation; nodule at 10 dpi (expanding nodule); nodule at 14 dpi (actively-fixing nodule), and 28 dpi (senescing nodule). Additional samples were collected from nodules that were re-supplied with nitrogen at 14 dpi, to suppress nitrogen fixation.
Nodule Development 2 Publicly available RNA-seq dataset from LIPM-INRA-CNRS was collected from root nodules at 10 or 15 dpi after inoculation with S. meliloti (Roux et al. 2014, DOI:10.1111/tpj.12442).
Nodule Development 3 Publicly available RNA-seq dataset from UCDAVIS was collected from a time-course of rhizobial infection events within the first 48 hours post-inoculation (hpi) (Larrainzar et al. 2015, DOI:10.1104/pp.15.00350).
Plant Tissues RNA-seq libraries were prepared from different plant tissues: root, leaf, leaf bud, pod, flower, petiole, and bare stalk collected at different stages.
Salt stress RNA-seq libraries were prepared from root and shoot tissues of plants grown under salt treatment (NaCl) collected after 25 days.
Symbiotic interactions 1 Publicly available RNA-seq dataset from LIPM-INRA-CNRS was collected from P-starved root tissue treated with sulfated or non-sulfated synthetic mycorrhizal lipochitooligosaccha$
Symbiotic interactions 2 Publicly available RNA-seq dataset from Garcia et al. 2017 (DOI: 10.1104/pp.16.01959) was collected from M. truncatula roots inoculated or not with the arbuscular mycorrhizal fungus Rhizophagus irregularis and watered with a high (3.75 mM) or low (0.05 mM) potassium solution for 6 weeks.
Symbiotic interactions 3 Publicly available RNA-seq dataset from from Jardinaud et al. 2016 (DOI: 10.1104/pp.16.00711) was collected from root epidermis after 4 or 24h treatment with Nod factors or mock treatment in n order to analyze very early symbiotic stages.
Symbiotic interactions 4 Publicly available RNA-seq dataset from from Luginbuehl et al 2017 (DOI 10.1126/science.aan0081) was collected from M. truncatula roots inoculated or not with the arbuscular mycorrhizal fungus Rhizophagus irregularis (8, 13 and 27 dpi).
Symbiotic interactions 5 Publicly available RNA-seq dataset from Zeijl et al 2015 (DOI http://dx.doi.org/10.1016/j.molp.2015.03.010) was collected from M. truncatula roots inoculated with Rhizobia meliloti.