|
| Status |
Public on Oct 10, 2014 |
| Title |
Control root 650-5 |
| Sample type |
SRA |
| |
|
| Source name |
Control root 650
|
| Organism |
Eucalyptus grandis |
| Characteristics |
strain: no fungus
tissue: control root
co2 concentration (ppm): 650
|
| Growth protocol |
For plant 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 or SI-12) was transferred directly on top of the plant root. The plates were closed using 2/3 electricians tape and 1/3 micropore tape. The micropore tape was used to ensure free gas exchange. Contiguity between CO2 levels in the petri dishes and the external environment was verified using a WMA-4 CO2 analyzer (PP Systems) according to manufacturers instructions. Inoculated plates were placed at a 45 degree angle in plant growth chambers (GC20 BDAF; Biochambers; Canada) under a temperature regime with a daytime high of 30oC and a nighttime low of 22o166 C and constant level of either 400 ppm CO2 or 650 CO2. Non-mycorrhizal (NM) control E. grandis plants grown axenically were treated identically for the same length of time and under the same conditions. Plates were left to incubate for 1 month. Root tissues were harvested directly within the chambers to prevent a drop in CO2 levels and were 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 |
This sample is from control roots. It is the fifth of five 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
Reads were aligned to the Eucalyptus grandis (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9) reference transcripts (primarytranscriptsonly) using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Eucalyptus grandis (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9)
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample
|
| |
|
| Submission date |
Oct 09, 2014 |
| Last update date |
May 15, 2019 |
| 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 |
GPL19281 |
| Series (1) |
| GSE62227 |
Elevated carbon dioxide alters the interaction between Eucalyptus grandis and Pisolithus microcarpus through a complex shift in the root transcriptome |
|
| Relations |
| BioSample |
SAMN03103635 |
| SRA |
SRX730472 |
