|
| Status |
Public on Nov 18, 2020 |
| Title |
Si9 ECM-1 |
| Sample type |
SRA |
| |
|
| Source name |
ECM
|
| Organisms |
Eucalyptus grandis; Pisolithus microcarpus |
| Characteristics |
tissue: ectomycorrhiza
colonization experiment: P. microcarpus Si9 fungal mycelium was transferred directly on top of the plant root
|
| Growth protocol |
For colonization experiments, individual 1 month old E. grandis seedlings were transferred to ½ strength MMN medium with 0.1% glucose in a 9 cm Petri dish and a single 0.25 cm2 160 square of fungal mycelium (Pisolithus microcarpus Si-9, MW3, R4 or R10) was transferred directly on top of the plant root. Inoculated plates were placed at a 45 degree angle in plant growth chambers (GC20 BDAF; Biochambers; Canada). Plates were left to incubate for 1 month. Root tissues were harvested frozen immediately at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Plant Kit using the RLC lysis buffer supplemented with 25 mg/mL PEG 8000 and following manufactuers instructions thereafter. RNA quantity was analyzed using the QuBit broad spectrum RNA kit as per manufacturers instructions and RNA quality was verified using the BioAnalyzer platform (Agilent Technologies Inc.).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the University of Western Sydney Next Generation Sequencing Facility (Richmont,Australia)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Pisolithus microcarpus x Eucalyptus grandis
This sample is from ectomycorrhizal roots. It is the first of two biological replicates used in this experiment.
|
| Data processing |
Illumina sofware was used by by the University of Western Sydney Next Generation Sequencing Facility to generate fastq raw data files
Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the reference transcripts available at JGI (Pisolithus microcarpus 441; https://mycocosm.jgi.doe.gov/Pismi1/Pismi1.home.html) using CLC Genomics Workbench v12 (Qiagen).
Genome_build: Pisolithus microcarpus 441; https://mycocosm.jgi.doe.gov/Pismi1/Pismi1.home.html
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads and TPM values for each sample
|
| |
|
| Submission date |
Jul 30, 2020 |
| Last update date |
Nov 19, 2020 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
annegret.kohler@inrae.fr
|
| Phone |
+33 (0)383 394072
|
| Organization name |
INRAE
|
| Department |
UMR 1136
|
| Lab |
Interactions Arbres/Micro-organismes
|
| Street address |
Centre INRAE Grand Est Nancy
|
| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
| |
|
| Platform ID |
GPL19282 |
| Series (1) |
| GSE155420 |
Gene expression analyses of four Pisolithus microcarpu strains: Si9, MW3, R4 and R10. Gene expression in Eucalyptus grandis mycorrhizal root tip was compared to gene expression in free-living mycelium for each strain. |
|
| Relations |
| BioSample |
SAMN15677603 |
| SRA |
SRX8850961 |
