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Series GSE216133 Query DataSets for GSE216133
Status Public on May 03, 2023
Title PAO1 Hfq-V RIL-seq
Organism Pseudomonas aeruginosa PAO1
Experiment type Other
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).
 
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.
 
Contributor(s) Gebhardt MJ, Melamed S, Dove SL
Citation(s) 37285605
Submission date Oct 19, 2022
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
 
Platforms (1)
GPL23999 Illumina NextSeq 500 (Pseudomonas aeruginosa PAO1)
Samples (12)
GSM6659105 PAO1 hfq-V EP RIL-IP replicate A
GSM6659106 PAO1 hfq-V EP RIL-IP replicate B
GSM6659107 PAO1 hfq-V EP RIL-IP replicate C
This SubSeries is part of SuperSeries:
GSE216135 PAO1 Hfq-V RIL-seq and RNA-seq
Relations
BioProject PRJNA892138

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE216133_Hfq-V_SP_all_PhrS_chimeras.bed.gz 1.3 Mb (ftp)(http) BED
GSE216133_RAW.tar 9.4 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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