|
| Status |
Public on May 22, 2018 |
| Title |
Agaricus bisporus 219 30P growth 27 days replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Mycelium colonized compost sample
|
| Organism |
Agaricus bisporus |
| Characteristics |
strain: 219 30P
sampling time: 27 days
sampling type: Mycelium colonized compost sample
|
| Treatment protocol |
After reaching the specific time point, compost samples were immediately stored at -20°C.
|
| Growth protocol |
Compost is based of wheat straw, horse and chicken manure, gypsum and water, according to commercial practice at CNC (Coöperatieve Nederlandse Champignonkwekersvereniging, Milsbeek, The Netherlands). The composts were inoculated with 176 mL of wheat kernels (spawns) colonized by the different strains. The crates were incubated in a commercial composting tunnel for 17 d after which they were moved to mushroom breeding farm and covered by 5 cm of casing layer. The incubation was continued in a breeding chamber similar to large scale commercial mushroom production. Approximately 1 L samples were taken from the middle of the crates after 27 and 39 d from the introduction of the spawns into the compost and corresponding to pinning stage and the first flush, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using a CsCl gradient centrifugation (Patyshakuliyeva et al., 2014) from the duplicate compost samples of A. bisporus strains 065 BP-8, 219 30P, 245 AMA-7 and A15 collected at the primordial stage (27 d) and the first flush (39 d). RNA quantity and integrity were determined with RNA6000 Nano Assay (Agilent 2100 Bioanalyzer, Agilent Technologies, USA). Preparation of cDNA library and sequencing reactions were conducted in the BGI Tech Solutions Co., Ltd. (Hong Kong, China) as described previously (Patyshakuliyeva et al., 2015).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Adaptor sequences, reads with unknown bases (N) >10% and low quality reads (more than 50% of the bases with quality values<5%) were removed. Clean reads were mapped to the genome sequence using BWA/Bowtie (Langmead et al., 2009; Li and Durbin, 2010)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using RSEM tool (Li et al. 2009)
Genome_build: Agaricus bisporus var bisporus (H97) http://genome.jgi.doe.gov/Agabi_varbisH97_2/
Supplementary_files_format_and_content: Files include FPKM values for each sample.
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronald de Vries |
| E-mail(s) |
fungalphysiology@gmail.com
|
| Phone |
+ 31 (0)30 2122600
|
| Organization name |
Centre of fungal biodiversity
|
| Department |
fungal physiology
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19762 |
| Series (1) |
| GSE99928 |
The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates |
|
| Relations |
| BioSample |
SAMN07221119 |
| SRA |
SRX2910158 |
