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| Status |
Public on May 03, 2023 |
| Title |
PhrS pulse expression RNA-seq |
| Organism |
Pseudomonas aeruginosa |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. We subjected cells of P. aeruginosa strain PAO1 and a derivative of PAO1 harboring a C-terminal VSV-G epitope on Hfq to UV-irradiation, immune-precipitated the Hfq-RNA complexes, ligated neighboring RNA molecules together with RNA Ligase, and then purififed the resulting RNAs. These RNAs were converted into cDNA libraries and sequenced using the Illumina NextSeq platform and then subjected to RIL-seq analysis pipeline (version 0.78) to identify chimeric RNA molecules.
We also performed RNA-seq for PAO1 ∆phrS cells harboring an empty vector (pEV) or a vector expressing PhrS (pPhrS).
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| Overall design |
Applying RIL-seq to strains carrying chromosomally-encoded Hfq-VSVG for two different growth conditions.
Applying RNA-seq to strains lacking phrS and harboring an empty vector or a vector containing a copy of phrS.
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| |
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| Contributor(s) |
Gebhardt MJ, Melamed S, Dove SL |
| Citation(s) |
37285605 |
| |
| Submission date |
Mar 20, 2023 |
| Last update date |
Aug 02, 2023 |
| Contact name |
Michael J Gebhardt |
| Organization name |
University of Iowa
|
| Department |
Department of Microbiology and Microbiology
|
| Lab |
Gebhardt
|
| Street address |
431 Newton Road, 200A EMRB
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL33271 |
NextSeq 2000 (Pseudomonas aeruginosa) |
|
| Samples (9)
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA966772 |
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