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| Status |
Public on Jan 22, 2019 |
| Title |
Identification of variant distribution in ethanol-selected sRNA libraries |
| Organism |
Vibrio cholerae C6706 |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
In this study we subjected a library of synthetic sRNAs to multiple rounds of ethanol selection and analyzed changes in sRNA variant abundance by high-throughput sequencing.
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| Overall design |
A synthetic sRNA library was generated by randomizing the first nine nucleotides of a RybB scaffold. The library was put under control of the IPTG-inducible PL promoter on a broad host range plasmid backbone and transferred into V. cholerae ΔrpoE. For laboratory selection experiments, the initial ΔrpoE sRNA library and control strains (WT- pCtr, ΔrpoE-pCtr and ΔrpoE-pRybB) were grown to exponential phase and challenged with ethanol. Following 6h of incubation, cells were recovered on agar plates to test for survival. At least 1 million single clones were pooled to generate the enriched sRNA libraries, which were used as input for the next round of selection following the same protocol. High-throughput sequencing of the isolated plasmids after each selection step was used to determine library complexity and distribution of the sRNA variants.
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| Contributor(s) |
Peschek N, Hoyos M, Herzog R, Förstner KU, Papenfort K |
| Citation(s) |
31313835 |
| |
| Submission date |
Jan 16, 2019 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Kathrin Fröhlich |
| E-mail(s) |
kathrin.froehlich@uni-jena.de
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| Organization name |
Friedrich-Schiller-Universität Jena
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| Department |
Fakultät für Biowissenschaften, Bacterial RNA Biology
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| Lab |
AG Fröhlich
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| Street address |
Winzerlaer Straße 2
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| City |
Jena |
| State/province |
Thuringia |
| ZIP/Postal code |
07745 |
| Country |
Germany |
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| Platforms (1) |
| GPL26051 |
Illumina MiSeq (Vibrio cholerae C6706) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE125224 |
A conserved seed-pairing domain affords small RNA-mediated stress resistance in enterobacteria |
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| Relations |
| BioProject |
PRJNA515434 |
| SRA |
SRP179733 |
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