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

  • [C. arietinum (gene)]
  • Detail of Experiment mapped on Cicer arietinum ICC 4958 CaV2

Details

Nameglobal view of transcriptome dynamics during drought stress in different chickpea genotypes
DescriptionIn this study, we aim to present a global view of transcriptome dynamics during drought stress in different chickpea genotypes. We generated about 800 million high-quality reads from 14 libraries (control and stress samples for two chickpea genotypes for drought stress at two developmental stages) using Illumina high-throughput sequencing platform. We mapped the reads to the kabuli chickpea genome for estimation of their transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample for each genotype. Overall design: We collected roots of chickpea genotypes from vegetative and reproductive stage plants subjected to control (water) and drought (water withhelding till transpiration ratio reached 0.2) stress. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequenced data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were mapped to annotated chickpea genome using TopHat and fragments per exon kilobase per million (FPKM) was calculated using Cufflinks software for each gene in all the sample to measure their gene expression. Differential expression analysis was performed using Cuffdiff software. The differentially expressed genes during various stress conditions were identified.
ContactNational Institute of Plant Genome Research (NIPGR)
XrefPRJNA288321
Reference
Conditions8
SpeciesCicer arietinum
Metadata export .CSV   .JSON

Analysis

Mapped Genomes CaV2    
Expression Analysis Expression Profile /  Differential Expression /  Co-expression

Conditions

Name Genotype Mutation Stage Tissue Treatment Level Time Samples Xref Download alignments
50d_ICC1882_control ICC1882 50 d plants Control
  • 50d_ICC1882_control_1
  • 50d_ICC1882_control_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
50d_ICC1882_drought ICC1882 50 d plants Drought
  • 50d_ICC1882_drought_1
  • 50d_ICC1882_drought_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
50d_ICC4958_control ICC4958 50 d plants Control
  • 50d_ICC4958_control_1
 .bam    .bai    .csi   
50d_ICC4958_drought ICC4958 50 d plants Drought
  • 50d_ICC4958_drought_1
 .bam    .bai    .csi   
70d_ICC1882_control ICC1882 70 d plants Control
  • 70d_ICC1882_control_1
  • 70d_ICC1882_control_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
70d_ICC1882_drought ICC1882 70 d plants Drought
  • 70d_ICC1882_drought_1
  • 70d_ICC1882_drought_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
70d_ICC4958_control ICC4958 70 d plants Control
  • 70d_ICC4958_control_1
  • 70d_ICC4958_control_2
 .bam    .bai    .csi   
.bam    .bai    .csi   
70d_ICC4958_drought ICC4958 70 d plants Drought
  • 70d_ICC4958_drought_1
  • 70d_ICC4958_drought_2
 .bam    .bai    .csi   
.bam    .bai    .csi