|
| Status |
Public on May 20, 2023 |
| Title |
ICC4958 Drought Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Cicer arietinum |
| Characteristics |
condition: Drought
genotype: ICC4958
phenotype: drought-tolerant
tissue: root
age: 27 days old
|
| Treatment protocol |
Drought stress was imposed on 16 day old plants by withholding water for 11 days, control samples were watered on alternate days. The roots were harvested from both stress and control samples from 27 days old seedlings.
|
| Growth protocol |
Cicer arietinum ICC4958, ICC1882 seedling were grown in a growth chamber
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRI Reagent. RNA quantification was performed and quality was assessed using Agilent Bioanalyzer. cDNA libraries were prepared and sequencing was performed on Illumina HiSeq platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Transcriptome
|
| Data processing |
The FASTQ files obtained were pre-processed using NGS QC Toolkit (v2.3.3) to remove adapters and low-quality reads. Low-quality reads with Phred score >20 were filtered.
Filtered high-quality reads were mapped on the chickpea genome (v1.0) using TopHat2 pipeline (v2.1.1).
A consensus reference-guided assembly of the transcriptome data was generated using Cufflinks (v2.2.1).
Differential expression of genes was determined by Cuffdiff (v2.2.1).
Genome_build: Kabuli chickpea genome (v1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each gene in the drought sensitive and tolerant cultivars under control and drought conditions
|
| |
|
| Submission date |
Jan 05, 2022 |
| Last update date |
May 20, 2023 |
| Contact name |
Rohini Garg |
| E-mail(s) |
rohini.garg@snu.edu.in
|
| Phone |
09560056446
|
| Organization name |
Shiv Nadar University
|
| Street address |
Shiv Nadar University, NH - 91, Tehsil Dadri
|
| City |
Gautam Buddha Nagar |
| State/province |
UP |
| ZIP/Postal code |
201314 |
| Country |
India |
| |
|
| Platform ID |
GPL31174 |
| Series (1) |
| GSE193077 |
Gene expression profiling of drought-sensitive (ICC1882) and tolerant (ICC4958) chickpea genotypes |
|
| Relations |
| BioSample |
SAMN24650402 |
| SRA |
SRX13614733 |
