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| Status |
Public on Feb 06, 2015 |
| Title |
Ectomycorrhizal roots-3 |
| Sample type |
SRA |
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| Source name |
Ectomycorrhiza
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| Organism |
Piloderma croceum |
| Characteristics |
host: Quercus robur
tissue: Ectomycorrhiza
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| Growth protocol |
P. croceum (DSMZ 4824, ATCC MYA-4870) was cultivated at 23°C on MMN (modified Melin-Norkrans medium) agar 102 with 10 g l−1 glucose, in the dark, or under 16:8 h day-to-night-cycle (photon flux density 100 μmol m-2s-1). For ECM synthesis, a modified culture system of the oak clone DF159 (Quercus robur L.) established by Herrmann et al. was used. After eight weeks on agar or in ECM synthesis cultures, samples were submerged into liquid nitrogen and stored at -80°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the samples using the MasterPure Plant RNA Purification Kit (Epicentre, Hessisch Oldendorf, Germany) according to the manufacturer’s instructions. In total, 50 mg of fungal mycelium or ectomycorrhizas were used for each extraction. RNA quantity and quality were estimated using a NanoDrop spectrophotometer (Thermo Scientific, Passau, Germany), gel electrophoresis, and a Nano Chip in a Bioanalyzer 2100 (Agilent, Böblingen, Germany).
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
This sample is from ectomycorrhizal roots. It is the third of three biological replicates used in this experiment.
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| Data processing |
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned to Piloderma croceum- (http://genome.jgi-psf.org/Pilcr1/Pilcr1.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: Piloderma croceum (http://genome.jgi-psf.org/Pilcr1/Pilcr1.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
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| Submission date |
Dec 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
annegret.kohler@inrae.fr
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| Phone |
+33 (0)383 394072
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| Organization name |
INRAE
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| Department |
UMR 1136
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| Lab |
Interactions Arbres/Micro-organismes
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| Street address |
Centre INRAE Grand Est Nancy
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| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
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| Platform ID |
GPL19512 |
| Series (2) |
| GSE63925 |
Gene expression changes in Piloderma croceum-Quercus robur ectomycorrhizal roots compared to Piloderma croceum free-living mycelium |
| GSE63947 |
Transcriptome comparison of ectomycorrhizal, ericoid and orchid mycorrhizal fungi |
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| Relations |
| BioSample |
SAMN03253421 |
| SRA |
SRX798262 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1560397_PilcrECM-3.txt.gz |
238.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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