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| Status |
Public on Sep 02, 2019 |
| Title |
mycorrhiza 2 |
| Sample type |
SRA |
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| Source name |
mycorrhiza
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| Organisms |
Tricholoma matsutake; Pinus densiflora |
| Characteristics |
cell type: mycorrhiza
passages: co-clutred 6 months
strain: T. matsutake strain IS01, Pinus densiflora in Iwate
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| Growth protocol |
Mycorrhizal synthesis was carried out using 500mL polycarbonate bottle (Agri pot, TGK Co. Ltd., Tokyo) containing 100 mL of vermiculite: sphagnum moss (80:1 w/w) moisturized with MYPG liquid media. The bottles were autoclaved at 121°C for 20 minutes, cooled to room temperature, then inoculated with T. matsutake colony grown on MYPG plate as described below. Rim of fungal colony was cut into 1cm cubic blocks, and three blocks were inserted into the substrate of each bottle. After inoculation of T. matsutake mycelium blocks, these bottles were placed in an incubator at 23°C for 1 month without light. Consequently, one aseptic seedling was transplanted into the substrate, and bottles were placed in a growth chamber at 23°C with light condition until use.
T. matsutake mycelia was inoculated on MYPG agar plate for 6 months at 25˚C in the dark
fruiting body of T. matsutake collected in wild, Iwate prefecture, 39°56’ N, 141°14’ E
Pine seedlings were cultured using 500mL polycarbonate bottle (Agri pot, TGK Co. Ltd., Tokyo) containing 100 mL of vermiculite: sphagnum moss (80:1 w/w) moisturized with MYPG liquid media. The bottles were autoclaved at 121°C for 20 minutes. Consequently, one aseptic seedling was transplanted into the substrate, and bottles were placed in a growth chamber at 23°C with light condition until use.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from mycorrhiza and pine root werer extracted by modified CTAB method reported by chang et al. 1993. RNA from mycelia and fruiting body were extracted by RNeasy plant kit (Qiagen)
library was constracted by Truseq RNA-seq kit (illumina) following manifacture's protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
mycorrhiza co-cultured with pine root for 6 months
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| Data processing |
Data processing is carried out using clc genomics workbench v11.
Supplementary_files_format_and_content: .csv tab-delimited text files include RPKM values for each Sample
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| Submission date |
Mar 08, 2019 |
| Last update date |
Sep 03, 2019 |
| Contact name |
Yuichi Sakamoto |
| E-mail(s) |
sakamoto@ibrc.or.jp
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| Organization name |
Iwate Biotechnology Research Center
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| Department |
Department of Bioresource
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| Lab |
mushroom team
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| Street address |
Narita 22-174-4
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| City |
Kitakami |
| State/province |
Iwate |
| ZIP/Postal code |
024-0003 |
| Country |
Japan |
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| Platform ID |
GPL26269 |
| Series (1) |
| GSE128059 |
RNA-seq analysis to identify Tricholoma matsutake mycorrhiza specific gene |
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| Relations |
| BioSample |
SAMN10583662 |
| SRA |
SRX5167644 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3661016_mycorrhiza2.csv.gz |
148.6 Kb |
(ftp)(http) |
CSV |
| GSM3661016_mycorrhiza_vs_pine2.csv.gz |
399.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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