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Series GSE67758

Query DataSets for GSE67758

Status

Public on Dec 11, 2015

Title

Dual RNA-seq – High-resolution comparative Dual RNA-seq time-course

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

High-resolution comparative Dual RNA-seq time-course

Contributor(s)

Westermann AJ, Förstner KU, Amman F, Barquist LE, Schulte LN, Chao Y, Müller L, Reinhardt R, Stadler PF, Vogel J

Citation(s)

Submission date

Apr 10, 2015

Last update date

May 15, 2019

Contact name

Konrad U. Förstner

E-mail(s)

foerstner@zbmed.de

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 (2)

GPL18573	Illumina NextSeq 500 (Homo sapiens)
GPL20051	Illumina NextSeq 500 (Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344)

Samples (51)

More...

GSM1924754	ΔpinT infection 0 h replicate 1
GSM1924755	ΔpinT infection 0 h replicate 2
GSM1924756	ΔpinT infection 0 h replicate 3

GSM1924757	ΔpinT infection 2 h replicate 1
GSM1924758	ΔpinT infection 2 h replicate 2
GSM1924759	ΔpinT infection 2 h replicate 3
GSM1924760	ΔpinT infection 4 h replicate 1
GSM1924761	ΔpinT infection 4 h replicate 2
GSM1924762	ΔpinT infection 4 h replicate 3
GSM1924763	ΔpinT infection 8 h replicate 1
GSM1924764	ΔpinT infection 8 h replicate 2
GSM1924765	ΔpinT infection 8 h replicate 3
GSM1924766	ΔpinT infection 16 h replicate 1
GSM1924767	ΔpinT infection 16 h replicate 2
GSM1924768	ΔpinT infection 16 h replicate 3
GSM1924769	ΔpinT infection 24 h replicate 1
GSM1924770	ΔpinT infection 24 h replicate 2
GSM1924771	ΔpinT infection 24 h replicate 3
GSM1924772	Wild-type infection 0 h replicate 1
GSM1924773	Wild-type infection 0 h replicate 2
GSM1924774	Wild-type infection 0 h replicate 3
GSM1924775	Wild-type infection 2 h replicate 1
GSM1924776	Wild-type infection 2 h replicate 2
GSM1924777	Wild-type infection 2 h replicate 3
GSM1924778	Wild-type infection 4 h replicate 1
GSM1924779	Wild-type infection 4 h replicate 2
GSM1924780	Wild-type infection 4 h replicate 3
GSM1924781	Wild-type infection 8 h replicate 1
GSM1924782	Wild-type infection 8 h replicate 2
GSM1924783	Wild-type infection 8 h replicate 3
GSM1924784	Wild-type infection 16 h replicate 1
GSM1924785	Wild-type infection 16 h replicate 2
GSM1924786	Wild-type infection 16 h replicate 3
GSM1924787	Wild-type infection 24 h replicate 1
GSM1924788	Wild-type infection 24 h replicate 2
GSM1924789	Wild-type infection 24 h replicate 3
GSM1924790	Mock 2 h replicate 1
GSM1924791	Mock 2 h replicate 2
GSM1924792	Mock 2 h replicate 3
GSM1924793	Mock 4 h replicate 1
GSM1924794	Mock 4 h replicate 2
GSM1924795	Mock 4 h replicate 3
GSM1924796	Mock 8 h replicate 1
GSM1924797	Mock 8 h replicate 2
GSM1924798	Mock 8 h replicate 3
GSM1924799	Mock 16 h replicate 1
GSM1924800	Mock 16 h replicate 2
GSM1924801	Mock 16 h replicate 3
GSM1924802	Mock 24 h replicate 1
GSM1924803	Mock 24 h replicate 2
GSM1924804	Mock 24 h replicate 3

This SubSeries is part of SuperSeries:

Dual RNA-seq of diverse human, mouse and pig cell-types infected with various Salmonella strains

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE67758_Raw_gene_wise_quantifications_Human_and_Salmonella.csv.gz	13.2 Mb	(ftp)(http)	CSV
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record

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