Differential Expression

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Name Description Contact Reference Conditions
Transcriptome profiling for two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56). Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were sequenced using Illumina RNA-seq technology. USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. Jamie.ORourke@ars.usda.gov. Link #1 12
The aboveground and root tissues from the alfalfa genotypes NECS-141, Altet-4 and NF08ALF0006 grown at pH 7, pH4 and the presence of aluminum ions. NECS-141 is sensitive to Al stress while Altet-4 and NF08ALF0006 are tolerant to Al stress. For each genotype, shoot-tip cuttings were clonally propagated and grown on an MS rooting media at 0.55g/L of basal medium with vitamins (PhytoTechnology Labs #M519), 1ml Plant Preservative Mixture (PhytoTechnology Labs) and 12g/L Gelzan (Physiol. Plant. 1962. 15: 473-497) at pH 5.8 in a growth room (24⁰C with 18 h day length) for 13 days. Individual rooted cuttings were then transferred to growth vessels (15ml Falcon conical centrifuge tubes, Corning, Corning, New York) containing 4 mL of CaCl2 liquid media at either pH 7 without Al (control) or pH 4 with 100 µM AlCl3 (pH 4 + Al) as described in Khu et al. (Crop Sci. 2012. 52:161-167). The experiment consisted of three biological replicates with 12 individuals per replicate in a randomized complete block design. Roots and shoots were collected after exposure and growth at either pH 7 or pH4 +Al at two time-points: three hours and 96 hours. RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich Co., St. Louis, Missouri). RNA-Sequencing libraries were constructed using Illumina TruSeq RNA Sample Preparation v2 Guide, (Illumina, San Diego, California) and one μg total RNA from each replicate and each genotype. Libraries were then validated using the Agilent 2100 Bioanalyzer with the DNA 1000 assay and sequenced on Illumina HiSeq™ 2000 platform with six samples per lane. Maria Monteros (mjmonteros@noble.org) unpublished 24
The aboveground biomass of alfalfa genotypes with the WXP1 transcription factor (TF) and without the WXP1 (control), and F1 and backcrossed (BC) progenies were grown under well-watered and water-stressed conditions. Six-week-old clones (cuttings) were transplanted to pots (2.5 gallon pots with Metro-mix 350 and Quikrete all-purpose sand mixed 2:1 v/v) and randomly distributed to each watering treatment using a randomized complete block design with three replications. Treatments include: 1. Well-watered: 600 ml of 0.5X B&D solution (Broughton and Dilworth, 1971) during establishment. Each pot was then watered with 1.2 L of 0.5X B&D solution at day 11, 14, 21, 24 and 28; Treatment 2. Drought stress: No solution was added to any of the pots in this treatment for 28 days. The tissues from plants grown in all replications were harvested when the volumetric water content (VWC) was greater than 30% for the well-watered treatment and less than 12% for the drought treatment, flash frozen in liquid nitrogen and stored at -80⁰C. A total of 80 to 100 mg of ground tissue was placed in a pre-chilled 2 ml microfuge tube and used for RNA extraction with the Spectrum Plant Total RNA kit (Sigma-Aldrich Co., St. Louis, Missouri). The libraries were constructed using Illumina’s TruSeq RNA Sample Preparation v2 Guide (Illumina, San Diego, California), validated using the Agilent 2100 Bioanalyzer with the DNA 1000 assay and used for HiSeq™2000 sequencing with six samples per lane. Maria Monteros (mjmonteros@noble.org) unpublished 22
Maria Monteros (mjmonteros@noble.org) unpublished 24