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| Status |
Public on Feb 05, 2020 |
| Title |
Profile of mRNA transcriptomes of E. coli affected by antifungal agent ciclopirox |
| Organisms |
Escherichia coli; Escherichia coli K-12 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The identification of genes and regulatory pathways involved in the susceptibility to ciclopirox activity
Methods: mRNA profiles of ciclopirox treatment in wild-type strain using Illumina sequencing.
Results: Using an optimized data analysis workflow, we mapped about 1 million sequence reads per sample to the E. coli K-12 genome and identified 4,290 transcripts in wild-type with our without sublethal concentration of ciclopirox (12.5 ug/mL). Overall, this is the first genome-wide level analysis of ciclopirox as an antibacterial against Gram-negative bacteria and shown that >13 pathways were affected by ciclopirox with the change of expression level of >10 genes. Data analysis with CLRNASeq showed some differently expressed transcripts by ciclopirox treatment.
Conclusions: Our study represents the first detailed analysis of ciclopirox-affected transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
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| Overall design |
mRNA profiles of ciclopirox treatment with or without sublethal concentration in wild type (WT) were generated by deep sequencing using Illumina HiSeq 2500.
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| Contributor(s) |
Kim K |
| Citation(s) |
29654752 |
| Submission date |
Feb 20, 2018 |
| Last update date |
May 06, 2020 |
| Contact name |
Kwang-sun Kim |
| E-mail(s) |
kwangsun.kim@pusan.ac.kr
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| Phone |
+82-51-510-2241
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| Organization name |
Pusan National University
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| Department |
Chemistry
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| Street address |
63 beon-gil 2, Jangjeon-dng, Geumjeong-gu
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| City |
Busan |
| ZIP/Postal code |
46241 |
| Country |
South Korea |
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| Platforms (2) |
| GPL18133 |
Illumina HiSeq 2500 (Escherichia coli) |
| GPL24570 |
Illumina HiSeq 2500 (Escherichia coli K-12) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA434677 |
| SRA |
SRP133129 |
