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| Status |
Public on Mar 16, 2024 |
| Title |
AV1-1-1_FRAS210075995-1 |
| Sample type |
SRA |
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| Source name |
hypha
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| Organism |
Pyricularia oryzae |
| Characteristics |
cell type: hypha
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| Growth protocol |
For vegetative growth, the M. oryzae strains were cultured on a complete medium (CM, 6 g yeast extract, 6 g casein hydrolysate, 10 g sucrose, 20 g agar for solid medium) for 5 days at 25℃, then transfered in the liquid CM for 3 days in a shaking incubator at 25℃ and 110 rpm condition.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction was using a HiPure Universal RNA kit (r4130-02; Magen, China) according to the manufacturer’s instructions. 5 μg of total RNA was used for the construction of sequencing libraires.
RNA integrity and quantity were verified by Agilent 2100 Bioanalyzer (Agilent Technologies, CA) and Qubit 2.0 (Life Tecnologies, China), respectively. The cDNA library was sequenced using IIIumina sequencing platform (NovaSqu 6000) with 150 bo pair-end reads length and 300 bp insert size by Novogene Co. (Tianjin, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
From isolate AV1-1-1, Biological Replicate 1
AV1-1-1-1r
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| Data processing |
Illumina Casava1.8 software was used for basecalling.
The raw data was trimmed by fastp (v0.20.1) to remove adapter sequences and low-quality reads.
The clean reads were aligned to the 70-15 reference genome using HISAT2 (v2.2.1) with the default parameter settings.
Gene expression based on the 70-15 reference genome annotations was determined using stringtie (v2.0) with the default parameter settings.
Transcripts per Million (TPM) were calculated for representing the expression of each gene.
Assembly: 70-15 reference genome
Supplementary files format and content: Matrix table with TPM for every gene and every sample
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| Submission date |
Jun 02, 2022 |
| Last update date |
Mar 16, 2024 |
| Contact name |
lianyu lin |
| E-mail(s) |
lianyulin.bio@gmail.com
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| Phone |
15280002320
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| Organization name |
Zhejiang University
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| Street address |
Zijingang Campus of Zhejiang University,Yuhangtang Road No.866
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310012 |
| Country |
China |
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| Platform ID |
GPL32309 |
| Series (1) |
| GSE205351 |
Hide-and-seek game in pathogen genome: Transposon elements play an important role in shaping population diversification of rice blast fungus Magnaporthe oryzae |
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| Relations |
| BioSample |
SAMN28828518 |
| SRA |
SRX15572979 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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