|
| Status |
Public on Feb 13, 2021 |
| Title |
EED mycelia 2 days rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Pyricularia oryzae |
| Characteristics |
strain: EED
genotype: mutant
developmental stage: mycelia
time: 2 days
|
| 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).
Genome_build: MG8
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 12, 2021 |
| Last update date |
Feb 13, 2021 |
| Contact name |
Chuyu Lin |
| E-mail(s) |
12316066@zju.edu.cn
|
| Phone |
+86 13588301175
|
| Organization name |
Zhejiang University
|
| Department |
College of Agriculture and Biotechnology
|
| Lab |
Tao’s Lab
|
| Street address |
866#, Yuhangtang Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL29717 |
| Series (2) |
| GSE166688 |
Next generation sequencing of transcript abundance during growth mycelia in the Magnaporthe oryzae [RNA-Seq II] |
| GSE166690 |
Suppression of polycomb-mediated H3K27me3 epigenetically de-repressed the genome-wide expression of effectomes in the vegetative growth stage |
|
| Relations |
| BioSample |
SAMN17892345 |
| SRA |
SRX10086461 |
