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

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

Name	global view of transcriptome dynamics during salinity stress in different chickpea genotypes
Description	In this study, we aim to present a global view of transcriptome dynamics during salinity stress in different chickpea genotypes. We generated about 600 million high-quality reads from 16 libraries (control and stress samples for two chickpea genotypes for salinity 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 salinity (irrigated with 80 mM NaCl solution) 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.
Contact	National Institute of Plant Genome Research (NIPGR)
Xref	PRJNA288473
Reference	Garg R et al . 2016;
Conditions	8
Species	Cicer 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
reproductive_ICCV2_80mMNaCl	ICCV2		Reproductive plants		80 mM NaCl solution			reproductive_ICCV2_80mMNaCl_1 reproductive_ICCV2_80mMNaCl_2	SRR2081157 SRR2081158	.bam .bai .csi .bam .bai .csi
reproductive_ICCV2_water	ICCV2		Reproductive plants		water			reproductive_ICCV2_water_1 reproductive_ICCV2_water_2	SRR2081155 SRR2081156	.bam .bai .csi .bam .bai .csi
reproductive_JG62_80mMNaCl	JG62		Reproductive plants		80 mM NaCl solution			reproductive_JG62_80mMNaCl_1 reproductive_JG62_80mMNaCl_2	SRR2081153 SRR2081154	.bam .bai .csi .bam .bai .csi
reproductive_JG62_water	JG62		Reproductive plants		water			reproductive_JG62_water_1 reproductive_JG62_water_2	SRR2081151 SRR2081152	.bam .bai .csi .bam .bai .csi
vegetative_ICCV2_80mMNaCl	ICCV2		Vegetative plants		80 mM NaCl solution			vegetative_ICCV2_80mMNaCl_1 vegetative_ICCV2_80mMNaCl_2	SRR2081149 SRR2081150	.bam .bai .csi .bam .bai .csi
vegetative_ICCV2_water	ICCV2		Vegetative plants		water			vegetative_ICCV2_water_1 vegetative_ICCV2_water_2	SRR2081147 SRR2081148	.bam .bai .csi .bam .bai .csi
vegetative_JG62_80mMNaCl	JG62		Vegetative plants		80 mM NaCl solution			vegetative_JG62_80mMNaCl_1 vegetative_JG62_80mMNaCl_2	SRR2081145 SRR2081146	.bam .bai .csi .bam .bai .csi
vegetative_JG62_water	JG62		Vegetative plants		water			vegetative_JG62_water_1 vegetative_JG62_water_2	SRR2081143 SRR2081144	.bam .bai .csi .bam .bai .csi