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Series GSE67757 Query DataSets for GSE67757
Status Public on Dec 11, 2015
Title Dual RNA-seq – Pilot Dual RNA-seq
Organisms Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
Experiment type Expression profiling by high throughput sequencing
Summary Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity is shown to adjust the human response to replicating Salmonella, and have a pervasive impact on host RNA expression both inside and outside protein-coding regions including infection-specific alterations of an array of long noncoding RNAs. Our study provides a paradigm for a comprehensive RNA-based analysis of intracellular bacterial pathogens without their physical purification from a host and a new discovery route for hidden functions of pathogen genes.
Overall design Pilot Dual RNA-seq: Infection of HeLa-S3 cells with wild-type Salmonella; 2 time points (4 h, 24 h p.i.; each sorted into invaded host cells [GFP+] and non-infected bystanders [GFP-]) and the respective human (4 h mock, 24 h mock) or bacterial reference controls (0 h LB, 0 h input), respectively. Three biological replicates were taken.
Contributor(s) Westermann AJ, Förstner KU, Amman F, Barquis LE, Schulte LN, Chao Y, Müller L, Reinhardt R, Stadler PF, Vogel J
Citation(s) 26789254
Submission date Apr 10, 2015
Last update date May 15, 2019
Contact name Konrad U. Förstner
Organization name ZB MED - Information Centre for Life Sciences
Department Information Services
Lab Förstner Lab
Street address Gleueler Str. 60
City Cologne
State/province North Rhine-Westphalia
ZIP/Postal code 50931
Country Germany
Platforms (1)
GPL20050 Illumina HiSeq 2000 (Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344)
Samples (24)
GSM1655351 0 h WT LB replicate 1
GSM1655352 0 h WT input replicate 1
GSM1655353 4 h mock GFP- replicate 1
This SubSeries is part of SuperSeries:
GSE60144 Dual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains
BioProject PRJNA280840
SRA SRP057064

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

Supplementary file Size Download File type/resource
GSE67757_Raw_gene_wise_quantifications_Human_and_Salmonella.csv.gz 23.7 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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