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| Status |
Public on Jan 01, 2017 |
| Title |
RNA-sequencing data from Pseudomonas putida KT2440 wild-type and Hfq-tagged strain form co-immunoprecipitation experiment |
| Organism |
Pseudomonas putida |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The RNA-chaperone Hfq is a global post-transcriptional regulator in Bacteria, important especially for the fine-tuning of the gene expression when the environmental conditions change. We looked into sRNAome during the growth of Pseudomonas putida KT2440 and compared it to a strain without Hfq protein. Numerous sRNAs were upregulated at a specific point during the growth and many were affected in the Hfq absence. Further we identified Hfq-binding RNA transcripts with co-immunoprecipitation and experimentally validated 17 sRNAs. Many novel Hfq-binding sRNAs were identified and are directly or indirectly regulated by Hfq. In addition 1870 mRNAs were found to bind to Hfq during the growth. Together, 202 antisense and 355 intergenic sRNAs have been detected in this study, several of them being 3’UTR- or 5’UTR-derived, and IS-related.
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| Overall design |
12 samples were analyzed; two strains (wild type and Hfq-FLAG-tagged strain) were compared in 3 time points during the growth in LB medium in two replicates each
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| Contributor(s) |
Bojanovič K, Long KS |
| Citation missing |
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| |
| Submission date |
Aug 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Klara Bojanovic |
| E-mail(s) |
klara.bojanovic@gmail.com
|
| Phone |
004524653766
|
| Organization name |
Technical University of Denmark
|
| Department |
Novo Nordisk Foundation Center for Biosustainability
|
| Street address |
Building 220, Kemitorvet
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| City |
Kgs. Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
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| Platforms (1) |
| GPL22319 |
Illumina NextSeq 500 (Pseudomonas putida) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA338876 |
| SRA |
SRP082120 |
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