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| Status |
Public on Jul 17, 2024 |
| Title |
RNA interactome profiling in hypervirulent Klebsiella pneumoniae |
| Organism |
Klebsiella pneumoniae subsp. pneumoniae ATCC 43816 |
| Experiment type |
Other
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| Summary |
To map the Hfq-mediated RNA regulatory network in HvKP, we harnessed the LiRIP-seq approach recently established in our lab, which enabled global profiling of RNA-RNA interactomes in live bacteria. Transformation of the pBAD-t4rnl1 plasmid into Klebsiella allowed us to express T4 RNA ligase 1 for proximity-ligation of RNAs in vivo, followed by co-immunoprecipitation (coIP) to enrich the Hfq-bound RNA transcripts (singleton reads) and ligated RNA fragments (chimeras: sRNA-mRNA, sRNA-sRNA, etc).
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| Overall design |
LiRIP-seq was carried out in triplicate in cells at early stationary phase of growth in LB (OD600 of 3.0), with a monoclonal anti-FLAG antibody for IP and mouse IgG as a negative control. The resulting RNA samples were purified and subjected to Illumina paired-end sequencing.
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| Contributor(s) |
Chao Y, Wu K, Lin X |
| Citation(s) |
39138169 |
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| Submission date |
Sep 14, 2023 |
| Last update date |
Sep 12, 2024 |
| Contact name |
Kejing Wu |
| E-mail(s) |
wukejing104@126.com
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| Organization name |
Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platforms (1) |
| GPL33764 |
Illumina NovaSeq 6000 (Klebsiella pneumoniae subsp. pneumoniae ATCC 43816) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA1017475 |
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