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| Status |
Public on Feb 06, 2015 |
| Title |
Mycelium patches-1 |
| Sample type |
SRA |
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| Source name |
Mycelium patches
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| Organism |
Paxillus involutus |
| Characteristics |
tissue: Mycelium patches
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| Growth protocol |
Mycelium patches and mycorrhizas were prepared as described in Wright et al. In brief, ECM association between birch and P. involutus was synthesized using a cellophane-agar Petri-dish system. Seeds of birch were surface-sterilized and then transferred aseptically to water agar plates until germination occurred. Nine-d-old seedlings were aseptically transferred to the edge of 9-d-old colonies of P. involutus growing on sheets of autoclaved cellophane placed over MMN agar containing 5.55 m glucose. After 4 wk mycorrhizal seedlings were transferred to pots containing unamended sphagnum peat to which four plugs of P. involutus mycelium were added. These pots were enclosed within a propagator, to maintain high humidity, and placed in a growth chamber at a day/night temperature of 18/15°C with a 16-h photoperiod and 80% relative humidity for 4 wk. After approximately 3 wk, once the extramatrical mycelium had colonized approximately two-thirds of the microcosm, two nutrient patches were placed into each chamber in advance (1 cm) of the mycelial front. Each nutrient patch consisted of a shallow plastic dish filled with autoclaved fine quartz sand (Sigma-Aldrich Sweden AB, Stockholm, Sweden) to which 1.5 ml of 1 mM (NH4)2SO4 was applied initially. Subsequently, 0.5 ml of 1 mM (NH4)2SO4 was applied weekly for 4 wk to allow extensive hyphal development within the patch and the formation of mycelial rhizomorphs which link the mycelium within the nutrient patch to the mycorrhizal root tips.In order to obtain a sufficient sample for total RNA extraction, material of each tissue type was pooledfrom three microcosms to produce one biological replicate. All material was immediately frozen in liquid N2 and stored at−80°C until use.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was immediately isolated from each sample using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions, except that PEG6000 (20 mg ml−1) (Merck KgaA, Darmstadt, Germany) and β- mercaptoethanol (10 μl l−1) were added to the RLC buffer. Total RNA preparations were inspected using a BioAnalyzer and the Total RNA Nano Series II kit (Agilent).
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 free-living mycelium. It is the first of two 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 Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.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: Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.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 |
GPL19511 |
| Series (2) |
| GSE63924 |
Gene expression changes in Paxillus involutus- Betula pendula ectomycorrhizal roots compared to Paxillus involutus mycelium patches |
| GSE63947 |
Transcriptome comparison of ectomycorrhizal, ericoid and orchid mycorrhizal fungi |
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| Relations |
| BioSample |
SAMN03253401 |
| SRA |
SRX798253 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1560388_PaxinPatches-1.txt.gz |
206.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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