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Series GSE261860 Query DataSets for GSE261860
Status Public on Apr 12, 2024
Title High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq4 (InSPI2, hydrogen peroxide (H2O2), nitric oxide (NO), sodium hypochlorite (bleach))
Organisms Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Experiment type Other
Summary Salmonella enterica is comprised of genetically distinct “serovars”, that together provide an intriguing model for exploring the genetic basis of pathogen evolution. While the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi & Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.
 
Overall design This is a Rb-Tn-seq project using barcoded transposons to rapidly identify changes in gene fitness. We tested 4 Salmonella isolates against 25 stress conditions each. Tn libraries were grown to an OD~1, then back-diluted 1:50 into either a media control or stressor. The concentration of each stressor was optimized such that growth of the library decreased by ~30-50% on average. The Tn libraries were allowed to grow overnight, then DNA was extracted using a Qiagen gDNA extraction kit. A barcoding PCR was performed to amplify all Tn-associated barcodes and sent for Illumina sequencing on a Hiseq4000. Fitness changes were calculated according to published scripts. This submission includes experiments from Barseq round 2, including H2O2, NO, bleach.
 
Contributor(s) Wang BX, Monack DM
Citation(s) 38831009
Submission date Mar 18, 2024
Last update date Jun 28, 2024
Contact name Benjamin Wang
E-mail(s) bwang40@stanford.edu
Phone 9737522074
Organization name Stanford
Street address 299 Campus Drive
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platforms (4)
GPL34285 Illumina HiSeq 4000 (Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74)
GPL34286 Illumina HiSeq 4000 (Salmonella enterica subsp. enterica serovar Typhi str. Ty2)
GPL34287 Illumina HiSeq 4000 (Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150)
Samples (40)
GSM8153124 mv 4/74 time 0 replicate 1 [Barseq4]
GSM8153125 mv Ty2 time 0 replicate 1 [Barseq4]
GSM8153126 mv Para time 0 replicate 1 [Barseq4]
This SubSeries is part of SuperSeries:
GSE264519 High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection
Relations
BioProject PRJNA1089222

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Supplementary file Size Download File type/resource
GSE261860_barseq4_D23580_processed.csv.gz 247.5 Kb (ftp)(http) CSV
GSE261860_barseq4_ST474_processed.csv.gz 264.0 Kb (ftp)(http) CSV
GSE261860_barseq4_Ty2_processed.csv.gz 245.9 Kb (ftp)(http) CSV
GSE261860_barseq4_para9150_processed.csv.gz 233.4 Kb (ftp)(http) CSV
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