|
| Status |
Public on Jan 15, 2020 |
| Title |
mRNAs from Fusarium graminearum GZ03639 wild-type under toxoflavin condition |
| Sample type |
SRA |
| |
|
| Source name |
Fungal culture containing toxoflavin (100 mg l-1), wild-type
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain/background: GZ03639
genotype/variation: wild-type
treatment: toxoflavin
toxoflavin sensitivity: resistant
|
| Treatment protocol |
The filtrated mycelia were incubated in 50 ml of minimal medium with presence of toxoflavin 100 mg l-1 for 24 h at 200 rpm.
|
| Growth protocol |
Fusarium graminearum wild-type strain GZ03639 and toxoflavin-sensitive mutant strain (∆GzZC190) were grown in 50 ml of complete medium at 25°C with shaking at 200 rpm for 72 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The mycelia were grinding in liquid nitrogen and total RNAs were extracted with NucleoSpin RNA Plant Kit (Machey-Nagel GmbH & Co. KG) according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using an Illumina TruSeqTM RNA sample prep kit (Illumina), according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq2000 instrument at the National Instrumentation Center for Environmental Management (NICEM).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The filtered reads of raw data were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bamtoreadcount.
Reads per kilobase of exon per million mapped sequence reads were calculated for normalization.
RPK100M = 100 x RPKM
Genome_build: Fusarium graminearum PH-1 ASM24013v3
Supplementary_files_format_and_content: *txt: Tab-delimited text files include gene information, raw count, RPKM, and RPK100M for each Sample.
|
| |
|
| Submission date |
Jan 15, 2017 |
| Last update date |
Jan 16, 2020 |
| Contact name |
Jungwook Park |
| E-mail(s) |
jjuwoogi@pusan.ac.kr
|
| Organization name |
Pusan National University
|
| Department |
Microbiology
|
| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
|
| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17573 |
| Series (1) |
| GSE93640 |
RNA-seq analyses of Fusarium graminearum wild-type GZ03639 and toxoflavin-sensitive mutant under toxoflavin condition |
|
| Relations |
| BioSample |
SAMN06233262 |
| SRA |
SRX2494091 |
