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| Status |
Public on Mar 01, 2018 |
| Title |
Sclerotia-3 |
| Sample type |
SRA |
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| Source name |
Sclerotia
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| Organism |
Cenococcum geophilum 1.58 |
| Characteristics |
tissue: Sclerotia
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| Growth protocol |
Pine seeds (P. sylvestris provenance VS/Leuk (31/10) WSL) were superficially disinfected in a laminar flux hood by immersion in H2O2 for 30 min, followed by three rinses with sterile distilled water. The seeds were germinated in modified MMN medium with low nitrogen and phosphorus during seven days for observation of contamination. After seed germination, the plants were transferred to Petri dishes containing modified MMN and covered with a cellophane membrane (135 mm). Approximately ten agar disks containing fungal mycelium of C. geophilum 1.58 were placed in the vicinity of the roots. The dishes were incubated in a growth chamber at 25 °C with 16 h light/ day for 90 days. Pure cultures of C. geophilum in identical conditions were used as experimental controls. Extramatrical mycelium surrounding roots and emanating from pine ECMs was scratched from the cellophane using a scalpel and if present, sclerotia formed in these dishes were separately collected and also immediately frozen in liquid nitrogen.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from mycorrhizal roots, sclerotia, extramatrical mycelium and fungal controls were extracted with the RNeasy Plant Mini kit (Qiagen, Courtaboeuf, France), including a DNase I (Qiagen) treatment, according to the manufacturer’s instructions to eliminate traces of genomic DNA. Assays for the quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA) or Agilent 2100 Bioanalyzer system (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sclerotia-3
11307.8.200793.CCTCAGT-AACTGAG
This sample is from sclerotia. It is the third of three biological replicates used in this experiment.
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| Data processing |
Illumina sofware was used by the JGI to generate fastq raw data files
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline. Filtered reads from each library were aligned to the Cenococcum reference transcriptome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) using BBmap with only unique mapping allowed (parameters: ambig=toss strictmaxindel=4 minid=0.9). If a read mapped to more than one location, it was ignored. Raw reads as well as FPKM and TPM normalized gene counts were generated using bbmap.
Genome_build: Cenococcum geophilum 1.58 (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html)
Supplementary_files_format_and_content: tab-delimited text file including JGI Cenge3 Protein IDs, raw counts, FPKM and TPM normalised values
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| Submission date |
Jan 08, 2018 |
| Last update date |
Mar 01, 2018 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
[email protected]
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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 |
GPL24474 |
| Series (1) |
| GSE108866 |
Gene expression changes in Cenococcum geophilum 1.58-Pinus sylvestris ectomycorrhizal roots, sclerotia and extramatrical mycelium compared to Cenococcum geophilum free-living mycelium |
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| Relations |
| BioSample |
SAMN08326599 |
| SRA |
SRX3540834 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2915135_CengeSclerotia-3.txt.gz |
152.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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