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Series GSE152295 Query DataSets for GSE152295
Status Public on Apr 23, 2021
Title RNA Atlas of Bacterial Human Pathogens Uncovers Stress Dynamics Linked to Bacterial Infections
Organisms Borreliella burgdorferi; Campylobacter jejuni; Helicobacter pylori; Francisella tularensis; Pseudomonas aeruginosa; Legionella pneumophila; Acinetobacter baumannii; Neisseria gonorrhoeae; Neisseria meningitidis; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Yersinia pseudotuberculosis; Vibrio cholerae; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus epidermidis; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Streptococcus pyogenes; Enterococcus faecalis; Listeria monocytogenes; Mycobacterium tuberculosis; Burkholderia pseudomallei; Salmonella enterica; Achromobacter xylosoxidans; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476
Experiment type Expression profiling by high throughput sequencing
Summary Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. Initial analyses of the comprehensive data set showed that beside coding RNAs, known and yet unknown putative novel ncRNAs comprise a significant part of the responses. We also computed a scores for all genes to be used for predictions for their probability to be regulated at certain stresses. The core scores enabled identification of universal stress responders representing conserved gene products involved in basic mechanisms important for responses to multiple stresses. Further, the environmental specific core scores made it possible to predict functions of yet non-characterized and also hypothetical gene products. All data are collected in the PATHOGENEX interactive RNA atlas, which is made available to the research community providing ample opportunities for discovering new aspects of regulatory networks in pathogenic bacteria as well as identification of novel players critical for bacterial infectivity and maintenance of infections.
 
Overall design Stress response of 32 human bacterial pathogens to 11 infection relevant stress conditions.
 
Contributor(s) Avican K, Fällman M
Citation(s) 34078900
Submission date Jun 11, 2020
Last update date Jun 09, 2021
Contact name Kemal Avican
E-mail(s) [email protected]
Organization name Umea University
Department Department of Molecular Biology
Lab Maria Fällman's Lab
Street address Building 6L
City Umea
ZIP/Postal code 90187
Country Sweden
 
Platforms (30)
GPL17879 Illumina HiSeq 2500 (Mycobacterium tuberculosis)
GPL18133 Illumina HiSeq 2500 (Escherichia coli)
GPL19488 Illumina HiSeq 2500 (Helicobacter pylori)
Samples (1122)
GSM4610754 A. xylosoxidans under acidic stress - rep1
GSM4610755 A. xylosoxidans under acidic stress - rep2
GSM4610756 A. xylosoxidans under acidic stress - rep3
Relations
BioProject PRJNA638918
SRA SRP266954

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
GSE152295_ACHX_processed.txt.gz 1.3 Mb (ftp)(http) TXT
GSE152295_ACIB_processed.txt.gz 958.3 Kb (ftp)(http) TXT
GSE152295_AGGA_processed.txt.gz 584.8 Kb (ftp)(http) TXT
GSE152295_BBURG_processed.txt.gz 324.0 Kb (ftp)(http) TXT
GSE152295_BURK_processed.txt.gz 1.4 Mb (ftp)(http) TXT
GSE152295_Campy_processed.txt.gz 456.0 Kb (ftp)(http) TXT
GSE152295_ENTFA_processed.txt.gz 644.0 Kb (ftp)(http) TXT
GSE152295_EPEC_processed.txt.gz 1.1 Mb (ftp)(http) TXT
GSE152295_ETEC_processed.txt.gz 1.2 Mb (ftp)(http) TXT
GSE152295_FRAT_processed.txt.gz 499.2 Kb (ftp)(http) TXT
GSE152295_HINF_processed.txt.gz 404.5 Kb (ftp)(http) TXT
GSE152295_HPG27_processed.txt.gz 384.9 Kb (ftp)(http) TXT
GSE152295_HPJ99_processed.txt.gz 377.4 Kb (ftp)(http) TXT
GSE152295_KLEBS_processed.txt.gz 1.3 Mb (ftp)(http) TXT
GSE152295_LEGIP_processed.txt.gz 643.0 Kb (ftp)(http) TXT
GSE152295_Listeria_processed.txt.gz 730.2 Kb (ftp)(http) TXT
GSE152295_MRSA_processed.txt.gz 670.1 Kb (ftp)(http) TXT
GSE152295_MSSA_processed.txt.gz 649.3 Kb (ftp)(http) TXT
GSE152295_MTB_processed.txt.gz 1015.4 Kb (ftp)(http) TXT
GSE152295_NGON_processed.txt.gz 500.5 Kb (ftp)(http) TXT
GSE152295_NMEN_processed.txt.gz 618.8 Kb (ftp)(http) TXT
GSE152295_PSEUDO_processed.txt.gz 1.4 Mb (ftp)(http) TXT
GSE152295_SALMT_processed.txt.gz 1.2 Mb (ftp)(http) TXT
GSE152295_SEPI_processed.txt.gz 593.9 Kb (ftp)(http) TXT
GSE152295_SHIF_processed.txt.gz 998.6 Kb (ftp)(http) TXT
GSE152295_SPYO_processed.txt.gz 468.2 Kb (ftp)(http) TXT
GSE152295_SSUIS_processed.txt.gz 426.0 Kb (ftp)(http) TXT
GSE152295_STAGA_processed.txt.gz 490.5 Kb (ftp)(http) TXT
GSE152295_STRPN_processed.txt.gz 520.0 Kb (ftp)(http) TXT
GSE152295_UPEC_processed.txt.gz 1.1 Mb (ftp)(http) TXT
GSE152295_Vibrio_processed.txt.gz 865.8 Kb (ftp)(http) TXT
GSE152295_YPSTB_processed.txt.gz 1.0 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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