|
| Status |
Public on Apr 03, 2018 |
| Title |
JG11 Genotype Control 3 Reproductive stage |
| Sample type |
SRA |
| |
|
| Source name |
Chickpea Root tissue
|
| Organism |
Cicer arietinum |
| Characteristics |
cultivar: JG11(salt-tolerant)
Stage: Reproductive Stage
treatment: No Treatment
tissue: Root
|
| Treatment protocol |
Total RNA was extracted from root tissues using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions. The quality and quantity of isolated RNA were confirmed by using Nanodrop spectrophotometer (NanoDrop Technologies) and Agilent Bioanalyzer. mRNA was isolated from the tolatal RNA using Dynabead PolyA RNA isolation kit (Ambion).
|
| Growth protocol |
In this study, two parental lines which segregate for salt tolerance (JG 11) and salt sensitivity (ICCV 2) were subjected to the 40 mM NaCl treatment at two developmental stages. The experiment was set-up in Random Complete Block (RCBD) design including three biological replicates at control and stress conditions. The salt treatment was maintained at electrical conductivity of ~1 dS/m and plants were maintained at the field capacity of the sandy soil in glasshouse.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen RNeasy mini kit
The sequencing for root samples was performed by Ion-Proton PGM sequencer. Four samples were pooled together in equimolars on a sequencing chip to to generate single end reads.
The raw Fasta files generated by sequencing were obtained and were cropped and trimmed using q-trim command line tool to remove low-quality reads and adapter sequences. Followed by Alignment and differential expression studies.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
JG11_LC3
|
| Data processing |
quadtrim command line was used to remove low quality reads.
High quality filtered reads were aligned to the CDC frontier kabuli v2.6.3 (Edwards, D; 2016) using tophat2 (tophat-gcc/2.0.13)
To analyse gene expression, the accepted.hit.bam file obtained from tophat analyses was subjedted to the HTSeq to obtain the genes counts.
The gene counts from three biological replicates were subjected to DESeq2 analyses to obtain the differentially expressed genes. A gene was considered to be differentially expressed if the FDR values were less than 0.05.
|
| |
|
| Submission date |
Feb 05, 2018 |
| Last update date |
Apr 03, 2018 |
| Contact name |
Nitin Mantri |
| E-mail(s) |
nitin.mantri@rmit.edu.au
|
| Organization name |
RMIT University
|
| Department |
School of Science
|
| Street address |
Plenty Road
|
| City |
Bundoora |
| State/province |
Victoria |
| ZIP/Postal code |
3083 |
| Country |
Australia |
| |
|
| Platform ID |
GPL22390 |
| Series (1) |
| GSE110127 |
Differential Regulation of Genes Involved in Root Morphogenesis and Cell Wall Modification is Associated with Salinity Tolerance in Chickpea |
|
| Relations |
| BioSample |
SAMN08466434 |
| SRA |
SRX3648096 |
