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Status |
Public on Nov 28, 2019 |
Title |
Gyman-10m-2 |
Sample type |
SRA |
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Source name |
Gyman_10months
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Organism |
Gymnopus androsaceus |
Characteristics |
tissue: mycelium growth medium: pine needles time: 10 months
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Growth protocol |
A total of 24 microcosms were filled with 85g of sand and 11g of dry Scots pine needles (Pinus sylvestris) each and sterilised by gamma radiation. The needle litter contained 0.42% N, 50.6% C, had a C:N-ratio of 120 and a lignin concentration of approximately 25%. For each fungal species, twelve microcosms were inoculated through the addition of single needles that had been pre-colonized for 2 months on N-free agar cultures. After inoculation, 20 ml of 100 mM NH4Cl solution were added to all microcosms, to stimulate fungal growth. Sealed microcosms were incubated at 20 ºC and 4 replicates from each fungal species were harvested after 2, 5 and 10 months, shock frozen in liquid nitrogen, ground using mortar and pestle and stored at -80 ºC.
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from 800 mg of tissue per sample using the RNA PowerSoil Total RNA Isolation Kit (Mobio now Qiagen). Quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA). cDNA libraries were prepared for sequencing using standard Illumina protocols by GeT (Génopole Toulouse Midi-Pyrénées, Auzeville, France)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
This sample is from Gymnopus androsaceus mycelium grown on pine needles for 10 month. It is the second of three biological replicates used in this experiment.
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Data processing |
Illumina software was used by GeT (Génopole Toulouse Midi-Pyrénées, Auzeville, France) to generate fastq raw data files Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 9. Trimmed reads were aligned to the Gymnopus androsaceus v1 (https://mycocosm.jgi.doe.gov/Gyman1/Gyman1.home.html) reference transcripts using CLC Genomics Workbench 9 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Genome_build: Gymnopus androsaceus v1 (https://mycocosm.jgi.doe.gov/Gyman1/Gyman1.home.html) Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample
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Submission date |
Oct 24, 2019 |
Last update date |
Nov 29, 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 |
GPL27655 |
Series (1) |
GSE139333 |
Gymnopus androsaceus growth on pine needles |
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Relations |
BioSample |
SAMN13108453 |
SRA |
SRX7051490 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4138320_Gyman_M10T2.txt.gz |
282.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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