|
| Status |
Public on Aug 01, 2016 |
| Title |
Free-living mycelium-3 |
| Sample type |
SRA |
| |
|
| Source name |
Free-living mycelium
|
| Organism |
Cenococcum geophilum |
| Characteristics |
tissue: Free-living mycelium
|
| Growth protocol |
Free-living mycelium (FLM) was grown on agar Petri dishes containing Cg-Medium and covered by a cellophane membrane. ECM plants were produced after the protocol of Kipfer et al. 2012. Two-month-old P. sylvestris seedlings inoculated with C. geophilum were cultivated in pots (300ml, two plants per pot) in a growth chamber for 3 months before harvesting. To collect ECMs, the roots were washed under tap water, placed in cooled water and ECM root tips were sampled under a binocular loupe using forks and immediately put in tubes that were placed in liquid N. Tubes were stored at -80°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from free-living mycelium and from ectomycorrhizal root tips of C. geophilum/Pinus sylvestris using the RNAeasy Plant Mini Kit of Qiagen with DNase step and addition of 20 mg/ml polyethylene glycol to the RLC extraction buffer.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
This sample is from free-living mycelium. It is the third of three biological replicates used in this experiment.
|
| Data processing |
Illumina software was used by IGA to generate fastq raw data files
Reads were aligned to Cenococcum geophilum- (http://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of aligned reads (RPKM) were calculated.
Genome_build: Cenococcum geophilum (http://genome.jgi.doe.gov/Cenge3/Cenge3.home.html)
Supplementary_files_format_and_content: tab-delimited text files including transcript length,unique aligned reads, total aligned reads and RPKM values for each sample
|
| |
|
| Submission date |
Jun 30, 2016 |
| 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 |
GPL22097 |
| Series (1) |
| GSE83909 |
Gene expression changes in Cenococcum geophilum-Pinus sylvestris ectomycorrhizal roots compared to Cenococcum geophilum free-living mycelium |
|
| Relations |
| BioSample |
SAMN05332122 |
| SRA |
SRX1889819 |
