|
| Status |
Public on Feb 15, 2023 |
| Title |
SS-C1 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Cicer arietinum |
| Characteristics |
condition: Control
genotype: ICCV2
tissue: salinity
age: 18 days old
|
| Treatment protocol |
Salinity stress was given on 12 day old seedlings with 80mM NaCl on alternate days for 6 days. The roots were harvested from both stressed and control samples from 18 days old plants.
|
| Growth protocol |
Cicer arietinum ICCV2 and JG62 genotype seedlings were grown in 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 RNA-sequencing was performed on Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SS-C1
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 Kabuli 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).
Assembly: Kabuli chickpea genome (v1.0) (https://data.legumeinfo.org/Cicer/arietinum/genomes/CDCFrontier.gnm1.GkHc/) (BIOPROJECT:PRJNA175619)
Supplementary files format and content: Tab-delimited text file including FPKM values for genes in the stress sensitive and stress tolerant under control and salinity stress conditions.
|
| |
|
| Submission date |
May 24, 2022 |
| Last update date |
Feb 15, 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 |
GPL32287 |
| Series (2) |
| GSE204727 |
Gene expression profiling during salinity stress response in chickpea (RNA-Seq) |
| GSE204730 |
Salinity stress response in chickpea |
|
| Relations |
| BioSample |
SAMN28639382 |
| SRA |
SRX15438194 |
