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

  • [A. thaliana (transcript)]
  • Detail of Experiment mapped on Arabidopsis thaliana col Araport11

Details

NameGenome-wide analysis of specific alterations in transcript structure and accumulation caused by nutrient deficiencies in Arabidopsis thaliana.
DescriptionAlteration of transcript structure represents an important step of regulation of gene function. To analyze genome wide response of exon combination patterns under nutrient deficiencies in plants, we performed paired-end RNA sequencing (illumine HiSeq2000) for the roots of Arabidopsis thaliana (Col-0) exposed to deficiencies of 12 different nutrients (N, K, Ca, Mg, P, S, B, Fe, Mn, Zn, Cu, Mo) and un-exposed control plants. Transcripts were assembled and quantified, and the relative abundances of transcript isoforms in each gene were compared among nutrient deficient conditions. We eventually obtained global and comprehensive data of regulatory exon combinations affected by nutritional conditions.
ContactGraduate School of Agricultural and Life Sciences , the University of Tokyo
XrefPRJDB5141
Reference
Conditions13
SpeciesArabidopsis thaliana
Metadata export .CSV   .JSON

Analysis

Mapped Genomes Araport11    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
B Col-0 root
  • B_1
  • B_2
  • DRR070508 
  • DRR070521 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Ca Col-0 root
  • Ca_1
  • Ca_2
  • DRR070504 
  • DRR070517 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Ctrl Col-0 root
  • Ctrl_1
  • Ctrl_2
  • DRR070501 
  • DRR070514 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Cu Col-0 root
  • Cu_1
  • Cu_2
  • DRR070512 
  • DRR070525 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Fe Col-0 root
  • Fe_1
  • Fe_2
  • DRR070509 
  • DRR070522 
 .bam    .bai    .csi   
.bam    .bai    .csi   
K Col-0 root
  • K_1
  • K_2
  • DRR070503 
  • DRR070516 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Mg Col-0 root
  • Mg_1
  • Mg_2
  • DRR070505 
  • DRR070518 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Mn Col-0 root
  • Mn_1
  • Mn_2
  • DRR070510 
  • DRR070523 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Mo Col-0 root
  • Mo_1
  • Mo_2
  • DRR070513 
  • DRR070526 
 .bam    .bai    .csi   
.bam    .bai    .csi   
N Col-0 root
  • N_1
  • N_2
  • DRR070502 
  • DRR070515 
 .bam    .bai    .csi   
.bam    .bai    .csi   
P Col-0 root
  • P_1
  • P_2
  • DRR070506 
  • DRR070519 
 .bam    .bai    .csi   
.bam    .bai    .csi   
S Col-0 root
  • S_1
  • S_2
  • DRR070507 
  • DRR070520 
 .bam    .bai    .csi   
.bam    .bai    .csi   
Zn Col-0 root
  • Zn_1
  • Zn_2
  • DRR070511 
  • DRR070524 
 .bam    .bai    .csi   
.bam    .bai    .csi