|
| Status |
Public on Nov 29, 2023 |
| Title |
ash1set2 mycelia 2 days rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Pyricularia oryzae |
| Characteristics |
cell type: mycelia
genotype: ash1set2 mutant
|
| 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.
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
RNAs were sequenced separately at Novogene, using Illumina Hiseq X-Ten 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
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Nov 29, 2023 |
| Contact name |
mengting xu |
| E-mail(s) |
12116082@zju.edu.cn
|
| Phone |
19858122056
|
| Organization name |
mengtingxu
|
| Street address |
Zhejiang University
|
| City |
Hangzhou |
| State/province |
ZheJiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL29717 |
| Series (2) |
| GSE235261 |
Next Generation Sequencing of Two H3K36 methyltransferases during growth mycelia in the Magnaporthe oryzae |
| GSE235415 |
Two H3K36 methyltransferases differentially associate with transcriptional activity and Ash1 is required for facultative heterochromatin and transcriptional silencing |
|
| Relations |
| BioSample |
SAMN35815566 |
| SRA |
SRX20733074 |
