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| Status |
Public on Nov 29, 2023 |
| Title |
1617 mycelia 2 days rep3 |
| Sample type |
SRA |
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| Source name |
t1617
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| Organism |
Pyricularia oryzae |
| Characteristics |
cell line: t1617
cell type: mycelia
genotype: mutant
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| Growth protocol |
The Magnaporthe oryzae strains were grown on CM medium at 28℃ in the dark for 2 days, followed by growth under continuous lights for 5 days. Then taking 4-5 pieces of mycelia and culture them in liquid CM medium for 2 days.The mycelia were harvested by 2-3 layers of Miracloth.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mycelia cultured in the liquid CM for 2 days from three biological repeats using the TRIzol (Invitrogen, USA) reagent according to the manufacturer’s instruction.
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 NovaSeq 6000 |
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| Data processing |
RNAs were sequenced separately at Novogene, using Illumina NovaSeq 6000 with Hiseq-PE150 strategy.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The clean reads were mapped to the reference genome of M. oryzae (MSU release 7) using TopHat software with default settings (Daehwan Kim, 2013). For analysis of differential expression, the assembled transcripts from three independent biological replicates in the WT and deletion mutants were included and compared using Cuffdiff with default settings (Trapnell et al., 2010).
To calculate the significance of the overlap of two sets of genes, P value with Fisher’s exact test for overlapping was performed with online test (the total number of genes in the M. oryzae genome used was 14317). (http://nemates.org/MA/progs/overlap_stats.html).
Assembly: MG8
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Oct 31, 2023 |
| Last update date |
Nov 29, 2023 |
| Contact name |
mengting xu |
| E-mail(s) |
12116082@zju.edu.cn
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| Phone |
19858122056
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| Organization name |
mengtingxu
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| Street address |
Zhejiang University
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| City |
Hangzhou |
| State/province |
ZheJiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL32309 |
| Series (2) |
| GSE246677 |
Next Generation Sequencing of a repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae |
| GSE246679 |
Repressive H3K36me2 reader during growth mycelia in the Magnaporthe oryzae |
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| Relations |
| BioSample |
SAMN38052499 |
| SRA |
SRX22321993 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7874523_t1617-3.txt.gz |
400.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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