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Name Description Contact Reference Conditions
Drought RNA was obtained from Medicago truncatula non-inoculated roots (R) and root nodules (inoculated with Sinorhizobium meliloti) either subjected to drought for two (T2) or four (T4) days, or well-watered control (T0). Two biological replicates for each sample was obtained. Each biological replicate consisted of roots or nodules harvested from 10-12 plants. RNA obtained from root nodules contained both plant and bacterial RNA. Weronika Czarnocka (weronika_czarnocka@sggw.pl) Sanko-Sawczenko et al. 2019 (DOI 10.3390/ijms20051204) 4
Hormone treatment RNA-seq libraries were obtained from roots of Medicago truncatula A17 plants three days post germination. The seedlings were immersed in B&D full nutrient media (Ph 6.8) containing the hormones at different concentrations; 1 uM IAA (Auxin), 100 nM BAP (Cytokinin) and an equal volume of the solvent control (DMSO). The seedlings were placed in the dark for 3 hours after which the root tips were removed and 40-60 roots per replicate were used. Sonali Roy (sroy@noble.org) or Ivone Torres-Jerez (itjerez@noble.org) Unpublished 3
Macronutrient Deficiencies 1 RNA-seq libraries were prepared from roots and shoots 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. Thomas de Bang (tdb@plen.ku.dk) de Bang et al. 2017 (DOI 10.1104/pp.17.01096) 24
Macronutrient Deficiencies 2 RNA-seq libraries were prepared from roots and shoots of plants grown under full nutrition, and with no nitrogen or phosphorus collected after 22 days of germination. Pooja Pandey-Pant (pppant@noble.org) de Bang et al. 2017 (DOI 10.1104/pp.17.01096) 6
Nodule Development 1 RNA-seq libraries were obtained from roots and nodules 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. Rebecca Dickstein (Rebecca.Dickstein@unt.edu) or Vijay Veerappan (veerappanv@easternct.edu) de Bang et al. 2017 (DOI 10.1104/pp.17.01096) 7
Nodule Development 2 RNA-seq datasets from LIPM-INRA-CNRS were collected from root nodules at 15 dpi after inoculation with S. meliloti. LIPM-INRA-CNRS (weblipm@toulouse.inra.fr) Roux et al. 2014 (DOI 10.1111/tpj.12442) 5
Nodule Development 3 RNA-seq datasets from UCDAVIS were collected from a time-course of rhizobial infection events within the first 48 hours post-inoculation (hpi). UCDAVIS (drcook@ucdavis.edu) Larrainzar et al. 2015 (DOI 10.1104/pp.15.00350) 36
Nodule Development 4 M. truncatula plants (pDME-DMEi and pDME-GUS - control) were inoculated with Rhizobia meliloti. Pascal Gamas (pascal.gamas@toulouse.inra.fr) Satge et al. 2016 (DOI 10.1038/nplants.2016.166) 4
Plant Organs RNA-seq libraries were prepared from different plant organs: root, leaf, leaf bud, pod, flower, petiole, and bare stalk collected at different stages. Ivone Torres-Jerez (itjerez@noble.org) Unpublished 9
Salt Stress RNA-seq libraries were prepared from roots and shoots of plants grown under salt treatment (NaCl) collected after 25 days. Yun Kang (ykang@noble.org) Unpublished 8
Symbiotic Interactions 1 RNA-seq datasets from LIPM-INRA-CNRS were collected from P-starved root tissue treated with sulfated or non-sulfated Myc-LCOs for 3 hours. LIPM-INRA-CNRS (weblipm@toulouse.inra.fr) Camps et al. 2015 (DOI 10.1111/nph.13427) 3
Symbiotic Interactions 2 M. truncatula plants were 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. RNA-seq libraries were prepared from roots. Jean-Michel Ane (jeanmichel.ane@wisc.edu) Garcia et al. 2017 (DOI 10.1104/pp.16.01959) 4
Symbiotic Interactions 3 RNA-seq datasets from INRA-CNRS were collected from root epidermis after 4 or 24h treatment with Nod factors or mock treatment in order to analyze very early symbiotic stages. Pascal Gamas (pascal.gamas@toulouse.inra.fr) Jardinaud et al. 2016 (DOI 10.1104/pp.16.00711) 4
Symbiotic Interactions 4 M. truncatula plants (wild type and RAM1 mutant) were inoculated or not with the arbuscular mycorrhizal fungus Rhizophagus irregularis (8, 13 and 27 dpi). RNA-seq libraries were prepared from roots. Peter J. Eastmond (peter.eastmond@rothamsted.ac.uk) Luginbuehl et al. 2017 (DOI 10.1126/science.aan0081) 12
Symbiotic Interactions 5 M. truncatula plants (wild type and Mtcre1 mutant) were inoculated or not with Rhizobia meliloti 2011 Nod factors. RNA-seq libraries were prepared from roots. Arjan van Zeijl (rene.geurts@wur.nl) Zeijl et al. 2015 (DOI 10.1016/j.molp.2015.03.010) 4
Symbiotic Interactions & Root Development M. truncatula mRNA samples were obtained from roots after 12-72 hours of lateral root initiation. Segment of roots in 0-168 hours after applying Sinorhizobium meliloti in wild type (jemalong cultivar Jester) was compared with mock treatments. Samples of roots from cre-1,nin-1 mutants was collected after 12,24 hours after applying Sinorhizobium meliloti and 24 hours for lbd16-1, and lbd16/lbd11 mutants which were also compared with mock treated samples. The mRNA samples from overexpression of LBD......[More] Tak Lee (tak.lee@slcu.cam.ac.uk) Schiessl et al. 2019 (DOI 10.1016/j.cub.2019.09.005) 59
Symbiotic Interactions 6 M. truncatula plants (wild type and SUNN mutant) were inoculated or not with the arbuscular mycorrhizal fungus Rhizophagus irregularis. RNA-seq libraries were prepared from root and shoot tissues. Thomas de Bang (tdb@plen.ku.dk) Karlo et al. 2020 (DOI 10.1093/jxb/eraa193) 8