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| Status |
Public on Dec 19, 2014 |
| Title |
Vv primordia |
| Sample type |
SRA |
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| Source name |
Mushroom
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| Organism |
Volvariella volvacea |
| Characteristics |
strain: H1521
tissue: Fruiting body
Stage: primordia
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| Growth protocol |
Culture spawn was prepared by growing mycelium on (w/w) 84% cotton seed hull, 9% wheat bran, 1% light Calcium Carbonate, 1% lime, 1% bagasse with 60-65% of relative humidity. Fruiting body production of V. volvacea was carried out in bed load. The cultivation substrate was composed of 25.5kg straw, 1.5kg cattle manure, and 0.5kg lime in 1m2 areas. Firstly, add the dry straw on the wood bed per square, and spray four days continuously. Then sprinkled the cattle manure on the straw bed surface with the lime. Secondly, after pasteurization by heating at 65℃ for 24–34h and cooling to around 32℃, the cultivation substrate was inoculated with the culture spawns of V. volvacea strains. Each V. volvacea strains were randomly arranged to cultured in triplicate with 5cm gap. Culture about six days at the temperature 32-32℃ with ventilating 2-3 times every day. Thirdly, open all doors and windows ventilation and cooling, while playing the fruiting water. Continue to training 2-3 days, fruiting bodies (primordium) usually emerged, but in others they were delayed for 2-4 weeks after the spawn was introduced.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mycelia using pBIOZOL Plant Total RNA Extraction Reagent, according to the manufacturer’s protocol (BioFlux). The isolated RNA was treated with RNeasy plant mini kit to remove potential genomic DNA contamination, according to the manufacturer’s protocol (QIAGEN, Germany). RNA integrity and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (6 μg) from each development stage of V. volvacea was submitted to BGI-Shenzhen (Shenzhen, China) for library construction and sequencing.
Sequence tag preparation was carried out using the Illumina Gene Expression Sample Prep Kit according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
3'-tag digital gene expression (DGE)
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| Data processing |
Illumina Cluster Station and Illumina HiSeq™ 2000 instrument used for basecalling.
Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences are transformed into Clean Tags after certain steps of data-processing.
A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences.All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). ('t Hoen, Ariyurek, et al. 2008; Morrissy, Morin, et al. 2009).
Genome_build: V.volvacea strain PYd21 genome data
Supplementary_files_format_and_content: tab-delimited text files include tag sequences,tag number and TPM values for each strain.
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| Submission date |
Jan 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Baogui Xie |
| E-mail(s) |
mrcfafu@163.com
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| Phone |
+86-591-83789277
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| Fax |
+86-591-83789277
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| Organization name |
mrcfafu
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| Department |
Mycological Research Center
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| Street address |
Shangdian Road
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| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350002 |
| Country |
China |
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| Platform ID |
GPL16412 |
| Series (1) |
| GSE43297 |
Homeobox transcription factors involved in fruiting body development of Volvariella volvacea |
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| Relations |
| SRA |
SRX214333 |
| BioSample |
SAMN01882556 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1060232_Primordia_TagCopyNumber.txt.gz |
612.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data included within Sample table |
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