|
| Status |
Public on May 25, 2022 |
| Title |
Set1 mycelia 7 days rep3 |
| Sample type |
SRA |
| |
|
| Source name |
mycelia
|
| Organism |
Ustilaginoidea virens |
| Characteristics |
strain: Set1
genotype: mutant
developmental stage: mycelia
time: 7 days
|
| Growth protocol |
The WT and all transformed strains derived from the WT were cultured on PSA (potato sucrose agar, potato 200 g/L, sucrose 20 g/L and agar 20 g/L) plates at 28°C under dark conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from mycelia cultured in liquid PS for 7 d using the TRIzol (Invitrogen) reagent. Subsequently, cDNAs were synthesized with a reversely transcribed kit (TAKARA) 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 with Illumina Hiseq X-Ten with Hiseq-PE150 strategy by Novogene Corporation (Beijing, China).
The obtained reads were mapped to the Ustilaginoidea virens (UV-8b) genome using Hisat2 (version 2.1.0) with default settings and sorted by SAMtools (Version 1.9).
R v4.0.3 package DESeq2 (version 1.30.1) was used to identify genes that were differentially expressed between the WT and ∆Uvkmt2 mutant. Genes with at least a 2-fold change in expression level (log2Fold Change ≥ 1, P < 0.05) between the ∆Uvkmt2 mutant and WT were considered to be differentially expressed.
Assembly: UV-8b
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 18, 2022 |
| Last update date |
May 25, 2022 |
| Contact name |
Chuyu Lin |
| E-mail(s) |
[email protected]
|
| 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 |
GPL27887 |
| Series (1) |
| GSE203327 |
Next generation sequencing analysis of transcript abundance during growth mycelia in the rice false smut fungus Ustilaginoidea virens |
|
| Relations |
| BioSample |
SAMN28534755 |
| SRA |
SRX15337176 |
