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

  • [G. max (gene)]
  • Detail of Experiment mapped on Glycine max Wm82 Gm508Wm82a4V1

Details

NameGenes Differentially Expressed in Slow Wilting Phenotypes under a High Vapor Pressure Deficit
DescriptionThe purpose of this study is to compare transcriptome profiles of one fast wilting and two slow wilting genotypes under low- and high- vapor pressure deficit Experiments: Five differential expression analyses were performed. 1. Differences within the Hutchesen line for slow and fast wilting; 2. Differences within the PI471938 line for slow and fast wilting; 3. Differences within the PI416937 line for slow and fast wilting; Differences between Hutchesen, PI471938 and PI416937 (regardless of pheotype); 5. Comparison between all lines and all pheotypes Methods: RNASeq data was generated using the Illumina HiSeq. Data passing quality control was processed as follows: Alignment to reference genome Gmax_109 using Tophat2 followed by the Tuxedo pipeline (cufflinks, cuffmerge, cuffdiff). Overall design: Three cultivars, (wild-type Hutchesen and two parentla lines - PI471938 and PI416937; two conditions (normal and slow-wilting); two reps each for a total of 12 samples
ContactBCSC, BRC, NC State University
XrefPRJNA213009
Reference
Conditions6
SpeciesGlycine max
Metadata export .CSV   .JSON

Analysis

Mapped Genomes Gm275Wm82a2V1     Gm508Wm82a4V1    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
Hutchesen_highVPD Hutchesen fast wilting leaf high vapor pressure
  • Hutchesen_highVPD_1
  • Hutchesen_highVPD_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
Hutchesen_lowVPD Hutchesen fast wilting leaf low vapor pressure
  • Hutchesen_lowVPD_1
  • Hutchesen_lowVPD_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
PI416937_highVPD PI416937 slow wilting leaf high vapor pressure
  • PI416937_highVPD_1
  • PI416937_highVPD_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
PI416937_lowVPD PI416937 slow wilting leaf low vapor pressure
  • PI416937_lowVPD_1
  • PI416937_lowVPD_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
PI471938_highVPD PI471938 slow wilting leaf high vapor pressure
  • PI471938_highVPD_1
  • PI471938_highVPD_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
PI471938_lowVPD PI471938 slow wilting leaf low vapor pressure
  • PI471938_lowVPD_1
  • PI471938_lowVPD_2
 .bam    .bai    .csi   
.bam    .bai    .csi