NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE239504 Query DataSets for GSE239504
Status Public on Feb 20, 2024
Title Bacterial single cell RNA-seq unveils cyclic-di-GMP as an antitoxin critical for antibiotic tolerance in biofilm [scRNA-seq]
Organisms Staphylococcus aureus; Pseudomonas aeruginosa PAO1; Escherichia coli str. K-12 substr. MG1655
Experiment type Expression profiling by high throughput sequencing
Summary Biofilms are heterogeneous bacterial communities featured by high persister prevalence, responsible for antibiotic tolerance. However, the mechanisms underlying persister formation within biofilms remained ambiguous. Here, by developing and utilizing a ribosomal RNA depleted bacterial single-cell RNA-seq method, RiboD-mSPLiT, we resolved biofilm heterogeneity and discovered pdeI as a marker gene for persister subgroup within biofilms. Remarkably, our findings elucidated that PdeI upregulates cellular levels of c-di-GMP, which acts as an antitoxin to modulate the toxicity of toxin protein HipH. HipH localizes on nucleoid and functions as a potent DNase, inducing cells into a viable but non-culturable state. Conversely, c-di-GMP interacts with HipH, reducing its genotoxic effects and enabling cells to enter a persister state, resulting in drug tolerance. Importantly, by targeting this toxin-antitoxin system, we repressed drug tolerance in Uropathogenic Escherichia coli infections, offering promising therapeutic strategies against chronic and relapsing infections.
 
Overall design we performed a new single-cell library construction method for three species of bacteria: Escherichia coli MG1655, Pseudomonas aeruginosa PAO1, Staphylococcus aureus 25923 and verified the effect of different treatments during library construction on library data. Then we analysed two E.coli single-cell sequencing datas, because we found that by cluster analysis we can find biofilm's marker gene

** The submitter states that the study's data have undergone significant changes and are no longer accurately reflected in SuperSeries GSE239505 [Feb 20, 2024]. The correct data are in SuperSeries GSE260458. **
Web link https://assets.researchsquare.com/files/rs-3329601/v1/579c700c-8679-4c2a-9ee4-dff08841c51a.pdf?c=1700559269
 
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jul 28, 2023
Last update date Mar 01, 2024
Contact name Xiaodan Yan
E-mail(s) 2019206500042@whu.edu.cn
Phone 13283874287
Organization name Wuhan University
Department Medical Research Institute
Street address Donghu Road, No. 115, Wuchang District,
City Wuhan
State/province Hubei Province
ZIP/Postal code 430071
Country China
 
Platforms (3)
GPL26592 Illumina NovaSeq 6000 (Escherichia coli str. K-12 substr. MG1655)
GPL27158 Illumina NovaSeq 6000 (Staphylococcus aureus)
GPL28916 Illumina NovaSeq 6000 (Pseudomonas aeruginosa PAO1)
Samples (14)
GSM7666360 EC-24h-static-ΔΔ, replicate 1, scRNA-seq
GSM7666361 EC-24h-static-ΔΔ, replicate 2, scRNA-seq
GSM7666362 EC-3h-ΔΔ, replicate 1, scRNA-seq
This SubSeries is part of SuperSeries:
GSE239505 Bacterial single cell RNA-seq unveils cyclic-di-GMP as an antitoxin critical for antibiotic tolerance in biofilm.
Relations
BioProject PRJNA999602

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
GSE239504_ECOLI_rRNA_and_mRNA_reads.txt.gz 116.9 Kb (ftp)(http) TXT
GSE239504_PAO1_rRNA_and_mRNA_reads.txt.gz 132.6 Kb (ftp)(http) TXT
GSE239504_RAW.tar 1.5 Gb (http)(custom) TAR (of XLSX)
GSE239504_Result_of_correlation_analysis_between_mSPLiT_and_RiboD-mSPLiT.xlsx 129.3 Kb (ftp)(http) XLSX
GSE239504_Result_of_correlation_analysis_between_scRNA_and_bulk_RNA-seq_.xlsx 143.3 Kb (ftp)(http) XLSX
GSE239504_SA_rRNA_and_mRNA_reads.txt.gz 71.2 Kb (ftp)(http) TXT
GSE239504_computational_pipeline_readme.txt 13.3 Kb (ftp)(http) TXT
GSE239504_scripts.tar.gz 10.4 Kb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap