|
| Status |
Public on Feb 06, 2015 |
| Title |
Ectomycorrhizal roots-2 |
| Sample type |
SRA |
| |
|
| Source name |
Ectomycorrhiza
|
| Organism |
Suillus luteus |
| Characteristics |
host: Pinus sylvestris
tissue: Ectomycorrhiza
|
| Growth protocol |
Suillus luteus was grown for 7 days at 23C on sterilized cellophane sheets sitting in Fries medium plates (4 plugs/plate) and used further for inoculation. Free-living mycelium was harvested after 7 days of growth in the same Fries medium by peeling off the mycelium and immediately freezing it in an eppendorf in liquid N. Samples were then stored at -80C. Pinus sylvestris seeds were kindly provided by Office National des Forêts, France. Four hundred of them were rinsed in a sieve with sterile MQ water, soaked in 34ml of a 12% TWEEN20 solution for 20min, rinsed with distilled water, soaked in 10% H2O2 for 15 min, rinsed with distilled water, soaked in 70% ethanol for 5 min, rinsed with distilled water, and placed in a tray containing sieved, acid-washed and moistened perlite. Seedlings were grown for four weeks in a growth chamber (day:night regime of 18 h light at 22°C and 6 h dark at 15°C) and watered every week with Ingestad’s nutrient solution slightly modified to induce P limitation in the pine seedlings. The macronutrient weight proportions were 100 N:9 P:54 K:6 Ca:6 Mg:9 S. Suillus luteus was inoculated on Pinus sylvestris seedlings using the sandwich technique described in Van Tichelen & Colpaert. Mycorrhizal root tips were harvested on 40 days-old seedlings. Two sets of about 50 ECMs were harvested from 10 seedlings (5 seedlings each). Each tip was harvested with tweezers and immediately frozen in an eppendorf floating in liquid N after separation from the root.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For ECMs, total RNAs were extracted from the frozen material using the protocol of Chang et al. that is well adapted to high-polyphenol Pine samples. http://ipmb.sinica.edu.tw/affy/document/Pine_Tree_Method.pdf. For mycelium, 100 mg of frozen sample was extracted using the Plant RNA mini kit. RNA quality was checked using Bioanalyzer.
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 ectomycorrhizal roots. It is the second of two biological replicates used in this experiment.
|
| Data processing |
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned toSuillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.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 |
Dec 05, 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 |
GPL19513 |
| Series (2) |
| GSE63926 |
Gene expression changes in Suillus luteus- Pinus sylvestris ectomycorrhizal roots compared to Suillus luteus free-living mycelium |
| GSE63947 |
Transcriptome comparison of ectomycorrhizal, ericoid and orchid mycorrhizal fungi |
|
| Relations |
| BioSample |
SAMN03253413 |
| SRA |
SRX798266 |
