|
| Status |
Public on Dec 31, 2018 |
| Title |
ICC283 Genotype sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cicer arietinum L. Chickpea Leaf tissue
|
| Organism |
Cicer arietinum |
| Characteristics |
tissue: Shoot apical meristem stage
strain: ICC283
treatment: Drought stressed (DS)
|
| Treatment protocol |
Total RNA was extracted from leaf 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
|
| Growth protocol |
In this study, two different chickpeas (Cicer arietinum L.) genotypes ICC8261 (Drought tolerant) and ICC283 (Drought sensitive) seeds were grown in a glasshouse under controlled conditions. The field capacity of soils for control samples was 80% and 20% for drought. Plants were grown in 20 cm polypropylene pots containing 4 kg of soil under controlled environmental conditions with air temperature regulated between 23C and 28C (night/day). The experiment was a 3 X 2 X 2 completely randomised block design one-time point (Shoot apical meristem), two genotypes, and two treatment conditions). For each genotype, 6 pots were used and randomly designated to one of two treatments: Well-watered (WW) control and drought-stressed (DS).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen Rneasy mini kit
The sequencing for leaf samples was performed by Illumina HiSeq 1000 in one lane each to generate 2×150 base pair paired-end reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimmomatic command line was used to remove low quality reads.
High quality filtered reads were aligned to the Chickpea referemce genome (Cicer arietinum ASM33114v1) (Varshney et al., 2013) TopHat v2.1.1
To analyse gene expression, a consensus reference-guided assembly of the transcriptome data from all samples will be generated using Cufflinks (v2.0.2) and the genes exhibiting a significant difference between treatment and control samples (at least two-fold change with P-value ≤ 0.05) considered to be differentially expressed.
To process data from high-throughput sequencing the read count was performed by HTseq python package
To analyse the gene expression of leaf tissue samples two different R programming analysis methods were used, DESeq2 (Love et al. 2014a) and EdgeR (Robinson et al. 2010). A stringent cut-off (q –value 0.001 and log2 fold change 1.0), was used for selecting differentially expressed genes.
Genome_build: ASM33114v1
Supplementary_files_format_and_content: RNAseq.gene.counts, DESeq2 and EdgeR data
|
| |
|
| Submission date |
Oct 05, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL20619 |
| Series (1) |
| GSE104609 |
RNA sequencing of leaf tissues from two contrasting chickpea genotypes reveals mechanisms for drought tolerance |
|
| Relations |
| BioSample |
SAMN07739353 |
| SRA |
SRX3244515 |
