|
| Status |
Public on Jun 20, 2023 |
| Title |
Eucalypt_Ctrl_JW28 |
| Sample type |
SRA |
| |
|
| Source name |
Root tissue (axenic)
|
| Organism |
Eucalyptus grandis |
| Characteristics |
tissue: Root tissue (axenic)
cell type: Root
genotype: 2068
treatment: Axenic control
|
| Treatment protocol |
Once the E. grandis seedlings were two months old and the fungal cultures had grown for one month, the plants were separated into one of three treatment categories: (1) fungal-free controls whereby the seedlings were transferred onto new half-strength MMN medium; (2) ‘pre-symbiosis’ which involved the transfer of seedlings onto new half-strength MMN medium in indirect contact with fungal mycelium for 24 h by separating the two organisms by a permeable cellophane membrane; (3) ‘physical contact’ seedlings were transferred onto new half-strength MMN medium and then placed into direct contact with the active growing edge of a fungal colony and then samples were harvested at 24 h, 48 h, 1 week, and 2 week post-contact. These plates were then closed using micropore tape to allow for gas exchange with the external environment.
|
| Growth protocol |
Plants and fungus were grown on half-strength MMN medium ((pH 5.5; 1 g l−1 glucose) at 22–30°C night/day temperature with a 16 h light cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ISOLATE II Plant miRNA kit (Bioline, Sydney, Australia)
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Biol Rep 4
|
| Data processing |
Paired-end Illumina reads were quality trimmed using the CLC Genomics Workbench tool version 11.0 (CLC Bio/Qiagen) removing ambiguous nucleotides as well as low quality read ends. The quality cutoff (error probability) was set to 0.05, corresponding to a Phred score of 13. Trimmed reads of >40 bases were mapped using the RNA-Seq Analysis 2.16 package in CLC requiring >80% sequence identity over >80% of the read length; strand specificity was omitted.
Genes with at least two-fold expression change and FDR value ≤<=0.05 were considered significant. Multidimensional scaling (“plotMDS” function in edgeR) was applied to visualize gene expression profiles. Expression heatmaps were generated by hierarchically clustering based on average linkage of FPKM values with heatmap.2 function from gplots package
To check reliability of both expression data, we used the superSeq package which uses a subsampling approach to simulate and predict the number of differentially expressed genes at lower read depths and random sampling points from the original dataset. These subsampled reads are then extrapolated to predict the relationship between statistical power and read depth.
Genes from the time-series in planta assay from both fungal and the plant side were clustered into co-expression based modules using STEM (v1.3.11)
N/A
Assembly: https://phytozome-next.jgi.doe.gov/info/Egrandis_v2_0; https://mycocosm.jgi.doe.gov/Armlut1/Armlut1.home.html
Supplementary files format and content: Normalised read counts of all genes across all samples for E. grandis
Supplementary files format and content: Normalised read counts of all genes across all samples for A. luteobubalina
|
| |
|
| Submission date |
May 23, 2023 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Jonathan Michael Plett |
| E-mail(s) |
[email protected]
|
| Organization name |
Western Sydney University
|
| Department |
Hawkesbury Institute for the Environment
|
| Street address |
Bourke St. Entrance, Building L9
|
| City |
Richmond |
| State/province |
NSW |
| ZIP/Postal code |
2753 |
| Country |
Australia |
| |
|
| Platform ID |
GPL20030 |
| Series (1) |
| GSE233220 |
Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen |
|
| Relations |
| BioSample |
SAMN35329153 |
| SRA |
SRX20484427 |
