|
| Status |
Public on Jul 07, 2021 |
| Title |
Jimbour_R_3 |
| Sample type |
SRA |
| |
|
| Source name |
Roots
|
| Organism |
Cicer arietinum |
| Characteristics |
genotype: Jimbour
agent: Mesorhizobium ciceri
|
| Treatment protocol |
Actively growing cultures of M. ciceri (~10,000 CFU per plant) was applied to half of the chickpeas while a mock solution without rhizobia was applied to the other half. Chickpea roots were harvested and frozen in liquid nitrogen 3 days after addition of live M. ciceri cultures or mock controls.
|
| Growth protocol |
Chickpea seeds from three genotypes forming low numbers of nodules (Jimbour, Boundary, ICC11664) and three genotypes with high nodulation (ICC9002, ICC2072 and ICC1510) were sterilized in 10% bleach, rinsed in sterile water and planted into vermiculite for two weeks. Seedlings were transplanted to sterilized soil and acclimatised to the new soil for a day prior to inoculation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the chickpea roots (3 biological replicates per condition) using the Isolate II RNA Plant kit (Bioline, London, U.K.) according to manufacturer’s instructions.
RNA libraries were constructed using the SENSE total RNA-Seq library prep kit (Lexogen, Vienna, Austria)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
NovaSeq sequencing was performed at the Ramaciotti Centre for Genomics (University of New South Wales, Sydney, Australia)
Raw reads from the RNA-sequencing were trimmed and mapped to the C. arietinum genome (desi type - ICC4958) using CLC Workbench v.10. Genes that were not expressed or lowly expressed (<5 counts on average across each set of 3 replicates) were eliminated from the data set.
Genome_build: C. arietinum genome (desi type - ICC4958)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 30, 2020 |
| Last update date |
Jul 07, 2021 |
| Contact name |
Krista Plett |
| E-mail(s) |
k.plett@westernsydney.edu.au
|
| Organization name |
Western Sydney University
|
| Department |
Hawkesbury Institute for the Environment
|
| Street address |
Locked Bag 1797
|
| City |
Penrith |
| State/province |
NSW |
| ZIP/Postal code |
2751 |
| Country |
Australia |
| |
|
| Platform ID |
GPL29457 |
| Series (1) |
| GSE162321 |
Chickpea shows genotype-specific nodulation responses across soil nitrogen environment and root disease resistance categories |
|
| Relations |
| BioSample |
SAMN16955107 |
| SRA |
SRX9604723 |
