|
| Status |
Public on Feb 15, 2023 |
| Title |
ST-C1 small RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Cicer arietinum |
| Characteristics |
condition: Control
genotype: JG62
age: 18 days old
|
| Treatment protocol |
Salinity stress was given on 12 day old plants with 80mM NaCl for 6 days on alternate days. The roots were harvested from both stress and control samples from 18 days old seedlings.
|
| Growth protocol |
Cicer arietinum ICCV2 and JG62 seedlings were grown in growth chamber
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRI reagent and small RNA library was prepared using TruSeq small RNA sample Prep Kit according to manufacturer’s instruction.
Small RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ST-C1
total RNA
|
| Data processing |
The FASTQ files obtained from small RNA sequencing were processed to remove adapters and low-quality reads.
After quality control, the reads were collapsed into a unique read and read count for each sequence was calculated.
Unique reads were mapped to the Kabuli chickpea genome.
Assembly: Kabuli chickpea genome (v1.0) (https://data.legumeinfo.org/Cicer/arietinum/genomes/CDCFrontier.gnm1.GkHc/) (BIOPROJECT:PRJNA175619)
|
| |
|
| 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) |
| GSE204728 |
Small RNA sequencing during salinity stress response in chickpea (small RNA-Seq) |
| GSE204730 |
Salinity stress response in chickpea |
|
| Relations |
| BioSample |
SAMN28639356 |
| SRA |
SRX15438190 |
