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| Status |
Public on Feb 06, 2015 |
| Title |
Mycorrhizal roots-1 |
| Sample type |
SRA |
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| Source name |
Mycorrhizal roots
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| Organism |
Serendipita vermifera |
| Characteristics |
host: Arabidopsis thaliana
tissue: Mycorrhizal roots
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| Growth protocol |
Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70% ethanol, surface sterilized for 5 min with 6% sodium hypochlorite and washed 6 times for 5 min in sterile water. After stratification for 3 days at 4°C in the dark on 1/10 PNM medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16 h, 23°C, 350 μmol m-2 s-1; night: 8 h, 18°C). S. vermifera strain was grown on MYP (7 g malt extract, 1 g peptone, 0.5 g yeast extract and 12 g agar) agar plates or liquid MYP with 120 rpm shaking at 25°C. Seven-day-old S. vermifera culture was filtered through miracloth filter and the mycelium was washed with 0.9% NaCl. Mycelium was crushed for 10 seconds in fresh MYP using a sterile blender (Microtron MB 550, Kinematica AG). 20 ml of crushed mycelium was inoculated in 130 ml MYP and regenerated for 3 days at 25°C with 130 rpm shaking. For inoculation of S. vermifera with Arabidopsis, fourteen-day-old germlings were inoculated with 5 g crashed fungal mycelium in 5 ml 0.9% NaCl solution for 2 h or 0.9% NaCl mock treated. S. vermifera inoculated plants, of approximately the same size, were transferred to square petri dishes containing 1/10 PNM and the roots were treated with either 1 ml of crushed fungal biomass (1 g/ml in 0.9% NaCl solution) per 20 seedlings or mock treated. The first four cm of the roots below the seed were excised and immediately frozen in liquid nitrogen for RNA extraction at 3, 7 and 14 days post inoculation. For each time point roots from 80 to 100 plants were harvested and the experiments were performed in 3 independent biological repetitions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 200 mg of ground material was extracted using TRIzol (Invitrogen, Karlsruhe, Germany) following the manufacturer’s instructions. Prior RNA extraction, plant materials harvested at 3, 7 and 14 dpi from the same independent biological experiment were pooled together. As control total RNA from 3 independent biological replicates of seven-day-old S. vermifera grown in MYP medium was used. RNA samples were additionally precipitated with ethanol. In brief, 1/10 volume of 3 M NaOAc and 3 volumes of ethanol were added to RNA solution. After incubation at - 20°C overnight, the RNA pellet was centrifuged at 13000 rpm for 30 min and washed once with 70% ethanol (diluted in DEPC ddH2O) and spin down for 10 min. The RNA pellet was then air-dried and resuspended in RNase-free water with a final concentration of 1 μg/μl. Purity and quantity of RNA samples were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer following the manufacturer’s protocol (Agilent, Santa Clara, USA).
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 mycorrhizal roots. It is the first 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 Sebacina vermifera (http://genome.jgi-psf.org/Sebve1/Sebve1.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: Sebacina vermifera (http://genome.jgi-psf.org/Sebve1/Sebve1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include 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 |
GPL19510 |
| Series (2) |
| GSE63923 |
Gene expression changes in Sebacina vermifera- Arabidopsis thaliana mycorrhizal roots compared to Sebacina vermifera free-living mycelium |
| GSE63947 |
Transcriptome comparison of ectomycorrhizal, ericoid and orchid mycorrhizal fungi |
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| Relations |
| BioSample |
SAMN03253408 |
| SRA |
SRX798250 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1560385_SebveMyc-1.txt.gz |
168.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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