|
| Status |
Public on Feb 01, 2017 |
| Title |
Inoculated_2d_1 |
| Sample type |
SRA |
| |
|
| Source name |
Inoculated mycelium 2 days
|
| Organism |
Hebeloma cylindrosporum |
| Characteristics |
strain: TV98 IV3
protocol: in contact with Pinus pinaster rotts
time point: 2 days
|
| Growth protocol |
For experiments focusing on pre-infectious stages of the interaction, seedling roots were inoculated by dipping them into a fast-growing mycelial homogenate in the Melin-Norkrans medium. Two inoculated seedlings were placed in each Petri dish and inoculation was further improved by pouring 50µl of fungal homogenate at the surface of each tap root. Control free-living mycelia were obtained by pouring, in the absence of host plant, the homogenate used as inoculum in Petri dishes filled with the same Melin-Norkrans medium as the one used for co-cultures. Inoculated seedlings were grown at 22 ± 1°C under 16 h photoperiodic illumination (80 mmol photons.m-2.s-1). Roots were protected from direct illumination using a black plastic film. After a two or four day co-culture, mycelia growing on the root surface were collected by gently scrubbing root surface with a spatula. Mycelia collected from 40 roots were suspended in 8 mL of sterile water which were centrifuged for 10 min at 10,800 g after adding 1 mL of 50% glycerol. The pellet was subsequently rinsed with 1 mL of sterile water and again centrifuged for 10 min at 15,000 g. The resulting pellet was frozen at -75°C and finally lyophilized before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lyophilized mycelia were ground in liquid nitrogen and total RNA was extracted using the "RNeasy Plant Mini Kit" (Qiagen, Courtaboeuf, France). PEG 8000 (20 mg.ml-1) and β-mercaptoethanol (10 µl.ml-1) were added in the RLC buffer (Qiagen). Samples were subsequently purified using the "Total RNA Purification, NucleoBond® RNA/DNA 80" kit (Macherey-Nagel, Hoerdt, France) by following the manufacturer’s recommendations.
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
This sample is from mycelium in contact with P.pinaster for 2 days. It is the first of tthree biological replicates used in this experiment.
|
| Data processing |
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to the Hebeloma cylindrosporum (http://genome.jgi-psf.org/Hebcy2) reference transcripts using CLC Genomics Workbench 8.5.1 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Hebeloma cylindrosporum (http://genome.jgi-psf.org/Hebcy2)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample
|
| |
|
| Submission date |
Jan 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
[email protected]
|
| 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 |
GPL19500 |
| Series (1) |
| GSE93184 |
The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation |
|
| Relations |
| BioSample |
SAMN06205394 |
| SRA |
SRX2464434 |
