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| Status |
Public on Sep 23, 2015 |
| Title |
first flush replicate2 |
| Sample type |
SRA |
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| Source name |
Mycelium colonized compost sample
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| Organism |
Agaricus bisporus |
| Characteristics |
strain: A 15
sampling time: first flush
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| Treatment protocol |
Mycelium colonized compost samples were collected at the different growth stages of A. bisporus. All samples were immediately frozen and stored at -20°C until being processed.
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| Growth protocol |
A. bisporus commercial heterokaryon strain A15 (Sylvan, USA) was used in this study. Phase I and II mushroom compost, which is based on wheat straw, horse and chicken manure, gypsum and water, were prepared according to commercial practice at CNC (Coӧperatieve Nederlandse Champignonwekersvereniging, Milsbeek, the Netherlands). Phase II compost was inoculated with A. bisporus spawns (Sylvan, USA) and incubated at 25°C for 16 days. Fully colonized compost was covered with casing layer (peat and lime) according to established commercial practice and incubated until first and second flushes of mushrooms were developed and harvested
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the collected compost samples using a CsCl gradient centrifugation method (Patyshakuliyeva et al., 2014). RNA integrity and quantity were checked with the RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Agaricus bisporus var bisporus (H97) v2.0 whole genome using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008.
Genome_build: Agaricus bisporus var bisporus (H97) v2.0
Supplementary_files_format_and_content: excel file include unique reads number, gene length, coverage, RPKM values and KEGG orthology annotation of genes for each sample.
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| Submission date |
Feb 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
miaomiao Zhou |
| E-mail(s) |
miaomiaozhou88@hotmail.com
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| Phone |
+ 31 (0)30 2122600
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| Organization name |
centre of fungal biodiversity, Utrecht, KNAW
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| Department |
fungal physiology
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
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| Platform ID |
GPL19762 |
| Series (1) |
| GSE65800 |
Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle |
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| Relations |
| BioSample |
SAMN03339311 |
| SRA |
SRX871411 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1606485_B4.Gene.rpkm.txt.gz |
547.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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