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Series GSE198436 Query DataSets for GSE198436
Status Public on Jun 21, 2023
Title Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks II
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Encounters between host cells and intracellular bacterial pathogens lead to complex phenotypes that determine the outcome of infection. Single-cell RNA-sequencing (scRNA-seq) are increasingly used to study the host factors underlying diverse cellular phenotypes. But current approaches do not permit the simultaneous unbiased study of both host and bacterial factors during infection. Here, we developed scPAIR-seq, an approach to analyze both host and pathogen factors during infection by combining multiplex-tagged mutant bacterial library with scRNA-seq to identify mutant-specific changes in host transcriptomes. We applied scPAIR-seq to macrophages infected with a library of Salmonella Typhimurium secretion system effector mutants. We developed a pipeline to independently analyze redundancy between effectors and mutant-specific unique fingerprints, and mapped the global virulence network of each individual effector by its impact on host immune pathways. ScPAIR-seq is a powerful tool to untangle bacterial virulence strategies and their complex interplay with host defense strategies that drive infection outcome.
 
Overall design Examination of differntially expressed genes between uninfected and WT/∆sifA infected BMDMs
 
Contributor(s) Heyman O, Yehezkel D, Blumberger N, Rosenberg G, Mattioli CC, Solomon A, Hoffman D, Ben-Moshe NB, Avraham R
Citation(s) 37399397
Submission date Mar 11, 2022
Last update date Oct 31, 2023
Contact name Noa Bossel Ben-Moshe
Organization name Weizmann
Street address Hertzl Street
City Rehovot
ZIP/Postal code 76100
Country Israel
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM5946842 uninfected_1
GSM5946843 uninfected_2
GSM5946844 uninfected_3
This SubSeries is part of SuperSeries:
GSE198728 Paired single-cell host profiling with multiplex-tagged bacterial mutants reveals intracellular virulence-immune networks
Relations
BioProject PRJNA815309

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

Supplementary file Size Download File type/resource
GSE198436_RAW.tar 1.1 Mb (http)(custom) TAR (of TXT)
GSE198436_data_matrix.txt.gz 238.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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