|
| Status |
Public on Oct 02, 2022 |
| Title |
EB2 treatment 1h 2 |
| Sample type |
SRA |
| |
|
| Source name |
PH-1
|
| Organism |
Fusarium graminearum |
| Characteristics |
cell line: PH-1
cell type: Hyphae
genotype: WT
treatment: Edeine B1
|
| Treatment protocol |
Edeine B1 was treated at 10 μg/mL on hyphae, and incubated 1 h,2 h, and 4 h.
|
| Growth protocol |
Spores of PH1 were incubated with potato dextrose broth (PDB) with agitation at 25℃ for 1day.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using easy-spinTM Total RNA Extraction Kit (Intron biotechnology)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
To check the quality of data before processing with analysis on raw data, FastQC (v0.11.7) was used.
Trimming was performed with various parameters for illumina paired-end or single-end using trimmomatic 0.38.
HISAT2 (ver 2.1.0) was used as a tool to map high throughput sequencing data to the reference genome, and graph FM index (GFM) was implemented based on the BWT extension of the graph.
Using StringTie (ver 2.1.3b), the potential transcript was assembled using the sequencing information mapped to the reference.
Assembly: ASM24013v3
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Sep 27, 2022 |
| Last update date |
Oct 02, 2022 |
| Contact name |
bomin Kim |
| E-mail(s) |
bobo890816@naver.com
|
| Organization name |
Korea reserch institute of chemical technology
|
| Street address |
141, Gajeong-ro
|
| City |
Daejeon |
| State/province |
Yuseong |
| ZIP/Postal code |
34114 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL28326 |
| Series (1) |
| GSE214312 |
Effect of edeine B1 in gene expression of Fusarium graminearum |
|
| Relations |
| BioSample |
SAMN31045358 |
| SRA |
SRX17725303 |
