LegumeIP V3: From Models to Crops - An Integrative Gene Discovery Platform for Translational Genomics in Legumes

  • [M. sativa (transcript)]
  • Detail of Experiment mapped on Medicago sativa CADL MsV1NR
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Details

NamepH and aluminum: parental genotypes
DescriptionThe 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.
ContactMaria Monteros (mjmonteros@noble.org)
Xref
Reference
Conditions24
SpeciesMedicago sativa
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Analysis

Mapped Genomes MsV1NR    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
A7R3 Altet-4 13d root control pH7 3h
  • A7R3_1
  • A7R3_2
  • A7R3_3
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A7R96 Altet-4 13d root control pH7 96h
  • A7R96_1
  • A7R96_2
  • A7R96_3
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A7S3 Altet-4 13d shoot control pH7 3h
  • A7S3_1
  • A7S3_2
  • A7S3_3
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A7S96 Altet-4 13d shoot control pH7 96h
  • A7S96_1
  • A7S96_2
  • A7S96_3
.bam    .bai    .csi   
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AAlR3 Altet-4 13d root acidic pH media;
alumimum(Al) 		pH4;
100 µM 		3h;
3h
  • AAlR3_1
  • AAlR3_2
  • AAlR3_3
.bam    .bai    .csi   
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AAlR96 Altet-4 13d root acidic pH media;
alumimum(Al) 		pH4;
100 µM 		96h;
96h
  • AAlR96_1
  • AAlR96_2
  • AAlR96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
AAlS3 Altet-4 13d shoot acidic pH media;
alumimum(Al) 		pH4;
100 µM 		3h;
3h
  • AAlS3_1
  • AAlS3_2
  • AAlS3_3
.bam    .bai    .csi   
.bam    .bai    .csi   
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AAlS96 Altet-4 13d shoot acidic pH media;
alumimum(Al) 		pH4;
100 µM 		96h;
96h
  • AAlS96_1
  • AAlS96_2
  • AAlS96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
N7R3 NECS-141 13d root control pH7 3h
  • N7R3_1
  • N7R3_2
  • N7R3_3
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N7R96 NECS-141 13d root control pH7 96h
  • N7R96_1
  • N7R96_2
  • N7R96_3
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N7S3 NECS-141 13d shoot control pH7 3h
  • N7S3_1
  • N7S3_2
  • N7S3_3
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.bam    .bai    .csi   
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N7S96 NECS-141 13d shoot control pH7 96h
  • N7S96_1
  • N7S96_2
  • N7S96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
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NAlR3 NECS-141 13d root acidic pH media;
alumimum(Al) 		pH4;
100 µM 		3h;
3h
  • NAlR3_1
  • NAlR3_2
  • NAlR3_3
.bam    .bai    .csi   
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NAlR96 NECS-141 13d root acidic pH media;
alumimum(Al) 		pH4;
100 µM 		96h;
96h
  • NAlR96_1
  • NAlR96_2
  • NAlR96_3
.bam    .bai    .csi   
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NAlS3 NECS-141 13d shoot acidic pH media;
alumimum(Al) 		pH4;
100 µM 		3h;
3h
  • NAlS3_1
  • NAlS3_2
  • NAlS3_3
.bam    .bai    .csi   
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NAlS96 NECS-141 13d shoot acidic pH media;
alumimum(Al) 		pH4;
100 µM 		96h;
96h
  • NAlS96_1
  • NAlS96_2
  • NAlS96_3
.bam    .bai    .csi   
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T7R3 60T180-4 13d root control pH7 3h
  • T7R3_1
  • T7R3_2
  • T7R3_3
.bam    .bai    .csi   
.bam    .bai    .csi   
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T7R96 60T180-4 13d root control pH7 96h
  • T7R96_1
  • T7R96_2
  • T7R96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
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T7S3 60T180-4 13d shoot control pH7 3h
  • T7S3_1
  • T7S3_2
  • T7S3_3
.bam    .bai    .csi   
.bam    .bai    .csi   
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T7S96 60T180-4 13d shoot control pH7 96h
  • T7S96_1
  • T7S96_2
  • T7S96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
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TAlR3 60T180-4 13d root acidic pH media;
alumimum(Al) 		pH4;
100 µM 		3h;
3h
  • TAlR3_1
  • TAlR3_2
  • TAlR3_3
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
TAlR96 60T180-4 13d root acidic pH media;
alumimum(Al) 		pH4;
100 µM 		96h;
96h
  • TAlR96_1
  • TAlR96_2
  • TAlR96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
TAlS3 60T180-4 13d shoot acidic pH media;
alumimum(Al) 		pH4;
100 µM 		3h;
3h
  • TAlS3_1
  • TAlS3_2
  • TAlS3_3
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi   
TAlS96 60T180-4 13d shoot acidic pH media;
alumimum(Al) 		pH4;
100 µM 		96h;
96h
  • TAlS96_1
  • TAlS96_2
  • TAlS96_3
.bam    .bai    .csi   
.bam    .bai    .csi   
.bam    .bai    .csi