|
| Status |
Public on Jul 23, 2017 |
| Title |
0.2 ppm deoxynivalenol |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial culture with 0.2 ppm deoxynivalenol
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K-12 substr. DH10B
condition: myxotoxin
toxin: deoxynivalenol
concentration: 0.2 ppm
|
| Growth protocol |
E. coli K-12 was incubated in 5 ml LB liquid for 16 h at 37°C with constant shaking, and then 100 µl of each myxotoxin dissolved in acetonitrile was added to each culture to a final concentration of 0.2, and 2 ppm. Additional incubation was performed for 2 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1 ml of each culture with the mycotoxin was centrifuged and total RNA was prepared using Hybrid-RTM kit (Gene All, Seoul, Korea) according to the manufacturer’s protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Texas, USA) was used to remove bacterial rRNA from the total RNA samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The reads were processed using BWA software.
Mapped reads per annotated gene were counted by Bam2readcount.
Reads per kilobase of gene per million mapped sequence reads (RPKM) were calculated for normalization.
Genome_build: Escherichia coli K-12 substr. DH10B ASM1942v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jul 23, 2014 |
| Last update date |
May 15, 2019 |
| 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 |
GPL14548 |
| Series (1) |
| GSE59682 |
Transcriptome analysis of Escherichia coli under deoxynivalenol and nivalenol conditions |
|
| Relations |
| BioSample |
SAMN02934130 |
| SRA |
SRX659741 |
