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Sample GSM4138320 Query DataSets for GSM4138320
Status Public on Nov 28, 2019
Title Gyman-10m-2
Sample type SRA
 
Source name Gyman_10months
Organism Gymnopus androsaceus
Characteristics tissue: mycelium
growth medium: pine needles
time: 10 months
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.
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)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
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.
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
 
Submission date Oct 24, 2019
Last update date Nov 29, 2019
Contact name Annegret Kohler
E-mail(s) annegret.kohler@inrae.fr
Phone +33 (0)383 394072
Organization name INRAE
Department UMR 1136
Lab Interactions Arbres/Micro-organismes
Street address Centre INRAE Grand Est Nancy
City Champenoux
ZIP/Postal code 54280
Country France
 
Platform ID GPL27655
Series (1)
GSE139333 Gymnopus androsaceus growth on pine needles
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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