GEO DataSets

(Submitter supplied) In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To faithfully detect Q-modification in RNAs from Schizosaccharomyces pombe and Shigella flexneri, Q-MaP-Seq was established and applied to tRNAs from S. pombe WT (AEP1) cells and Shigella flexneri WT cells and tgt∆ cells. Q-modification of in vitro-transcribed RNAs and RNAs isolated from S. more...

Organism:

Schizosaccharomyces pombe; Shigella flexneri

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16192 GPL30040

30 Samples

Download data: XLSX

(Submitter supplied) In this study, we probed factors that could influence Shigella pathogenesis. We show that in basic pH conditions, deoxycholate-induced biofilm formation and virulence of Shigella are attenuated. We utilized RNA-sequencing to investigate pathways enriched in bacterial cells in biofilms.

Organism:

Shigella flexneri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30595

6 Samples

Download data: TXT

(Submitter supplied) We compared the transcriptomes of S. flexneri strains expressing the diguanylate cyclase VCA0956 (derived from V. cholerae)

Organism:

Shigella flexneri 2a str. 2457T

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30069

6 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Pseudomonas putida; Yersinia pseudotuberculosis; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli K-12

Type:

Genome binding/occupancy profiling by high throughput sequencing

9 related Platforms

102 Samples

Download data: GFF

(Submitter supplied) Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. more...

Organism:

Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Yersinia pseudotuberculosis; Salmonella enterica

Type:

Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

14 Samples

Download data: GFF

(Submitter supplied) 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. more...

Organism:

Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans; Helicobacter pylori; Enterococcus faecalis; Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei; Campylobacter jejuni; Francisella tularensis; Acinetobacter baumannii; Neisseria gonorrhoeae; Escherichia coli; Shigella flexneri; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476

Type:

Expression profiling by high throughput sequencing

30 related Platforms

1122 Samples

Download data: TXT

(Submitter supplied) Transcriptional program of a WT and ipaD strain of Shigella flexneri modeling the off- and on-state of the T3SA in vitro were compared by RNA-Seq

Organism:

Shigella flexneri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25905

2 Samples

Download data: CSV

(Submitter supplied) S. flexneri infected Henle-407 cells were treated with and without 20 mM formate, RNA-seq was used to determine transcriptome changes

Organism:

Homo sapiens; Shigella flexneri 2a str. 2457T

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL25540

3 Samples

Download data: XLSX

(Submitter supplied) To explore what important role of PhoPQ TCS plays in Shigella virulence, the Agilent microarray technologies was used to compare the transcriptional profiles of Shigella flexneri 2a 301 and △phoPQ mutant strains at middle-log phase (6 h) or early-stationary phase (10 h) under LB growth conditions.

Organism:

Shigella flexneri

Type:

Expression profiling by array

Platform:

GPL24308

12 Samples

Download data: TXT

(Submitter supplied) Shigella flexneri is a facultative intracellular pathogen which is mainly responsible for endemic shigellosis in developing countries. In the present study, we demonstrated S.flexnerri was susceptible to furazolidone, a nitrofuran derivative that has been used as therapeutic regimen against a variety of gastro-intestinal bacterial infections. To identify the global transcriptional responses of S.flexnerri in response to furazolidone treatment, S.flexnrri was exposed to both subinhibitory and inhibitory concentrations of furazolidone and microarray analysis was used to examine gene expressions after both short and long period of incubation. more...

Organism:

Shigella flexneri

Type:

Expression profiling by array

Platform:

GPL5068

18 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Helicobacter pylori; Yersinia enterocolitica; Chlamydia trachomatis; Mycobacterium tuberculosis variant bovis; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Coxsackievirus B4; Coxsackievirus A20; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Proteus mirabilis; Streptococcus pyogenes; Mycobacterium gordonae; Trypanosoma cruzi; Caprine arthritis encephalitis virus; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Human rotavirus MP409; Paraburkholderia fungorum; Staphylococcus aureus A9635; Hepacivirus hominis; Klebsiella pneumoniae; Porphyromonas gingivalis; Mycobacterium avium subsp. paratuberculosis; Mycobacterium tuberculosis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Human herpesvirus 4 strain B95-8; Human immunodeficiency virus 1; Human herpesvirus 4 type 1; Coxsackievirus B4 (strain E2); Escherichia coli; Shigella flexneri; Haemophilus influenzae; Staphylococcus aureus; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human betaherpesvirus 6; human gammaherpesvirus 4; Human T-cell leukemia virus type I; Coxsackievirus A9; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Betapolyomavirus macacae

Type:

Protein profiling by protein array

Platforms:

GPL19701 GPL19692 GPL19700

29 Samples

Download data: XLSX

(Submitter supplied) The aim of the array was to determine the BXD2 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old BXD2 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:

Escherichia coli; Klebsiella pneumoniae; Proteus mirabilis; Porphyromonas gingivalis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mycobacterium gordonae; Mus musculus; Human betaherpesvirus 6; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Human herpesvirus 4 type 1; Human endogenous retrovirus K; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Coxsackievirus A9; Coxsackievirus B4 (strain E2); Betapolyomavirus macacae; Helicobacter pylori; Shigella flexneri; Yersinia enterocolitica; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human T-cell leukemia virus type I; Coxsackievirus A20; Torque teno virus; Prochlorococcus marinus str. MIT 9202; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Staphylococcus aureus A9635; Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Trypanosoma cruzi; Homo sapiens; Human herpesvirus 4 strain B95-8; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis

Type:

Protein profiling by protein array

Platform:

GPL19701

2 Samples

Download data: XLSX

(Submitter supplied) The aim of the array was to determine the B6 mouse sera IgG and IgM reactivity profile to linear peptide epitopes. Pooled sera from three 6-9 month old B6 mice was diluted at 1:200 for IgG specific analysis or 1:1000 for IgM specific analysis and incubated on a PEPperPRINT peptide microarray platform printed with peptide autoantigens

Organism:

Haemophilus influenzae; Lactobacillus delbrueckii subsp. bulgaricus; Mycobacterium avium; Mycobacterium tuberculosis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Human herpesvirus 4 strain B95-8; Human T-cell leukemia virus type I; Coxsackievirus A9; Prochlorococcus marinus str. MIT 9202; Coxsackievirus B4 (strain E2); Staphylococcus aureus A9635; Betapolyomavirus macacae; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Mus musculus; Human immunodeficiency virus 1; Human herpesvirus 4 type 2; Chlamydia pneumoniae; Human poliovirus 3 strain Sabin; Helicobacter pylori; Proteus mirabilis; Yersinia enterocolitica; Porphyromonas gingivalis; Mycobacterium gordonae; Human alphaherpesvirus 2; Hepatitis C virus isolate HC-J6; Human herpesvirus 4 type 1; Coxsackievirus A20; Torque teno virus; Paraburkholderia fungorum; Porphyromonas gingivalis W83; Mycobacterium avium subsp. paratuberculosis K-10; Chlamydia trachomatis; Streptococcus pyogenes; Mycobacterium tuberculosis variant bovis; Trypanosoma cruzi; Human betaherpesvirus 6; Human T-cell lymphotrophic virus type 1 (isolate MT-2); Coxsackievirus B4; Human adenovirus 12; Human endogenous retrovirus K; Human Endogenous Retrovirus IDDMK1,2-22; Human rotavirus MP409; Hepacivirus hominis

Type:

Protein profiling by protein array

Platform:

GPL19701

2 Samples

Download data: XLSX

(Submitter supplied) Investigate whole genome gene expression level changes in an S. flexneri ntrBC and nac mutants compared to wild type strain. NtrBC is a two component regulatory system, nac is a transcriptional activator Mutations in ntrBC and nac result in small plaque formation in Henle cell monolayers compared to wild type bacteria. Gene expression studies were pursued to identify the genes regulated by these transcriptional regulators.

Organism:

Shigella flexneri; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL14649

9 Samples

Download data: PAIR

(Submitter supplied) Comparison of wild type S. flexneri 2457T gene expression to deletion mutant of S. flexneri 2457T gene S4473 at three growth phases and intracellularly

Organism:

Shigella flexneri 2a str. 2457T; Escherichia coli; Shigella

Type:

Expression profiling by array

Platform:

GPL13175

14 Samples

Download data: CEL, CHP

(Submitter supplied) Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia albertii TW07627; Escherichia sp. TW11930; Escherichia sp. TW14264; Escherichia sp. TW14266; Escherichia coli O127:H6 str. E2348/69; Escherichia sp. RL325/96; Escherichia sp. TW14182; Shigella flexneri 2a str. 2457T; Escherichia coli CFT073; Escherichia coli 042; Escherichia coli str. K-12 substr. MG1655; Escherichia sp. TW09231; Escherichia sp. TW11588; Escherichia sp. TW11966; Escherichia sp. TW14265; Escherichia sp. TW14267; Escherichia sp. Z205; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia albertii; Escherichia sp. TW09254; Escherichia sp. TW09266; Escherichia sp. TW09276; Escherichia sp. TW09308; Escherichia sp. TW14263

Type:

Genome variation profiling by array

Platform:

GPL15851

50 Samples

Download data: GPR

(Submitter supplied) Global transcriptional responses of shigella flexneri to RNA poly merase inhibitor

Organism:

Shigella flexneri

Type:

Expression profiling by array

Platform:

GPL14728

36 Samples

Download data: GPR

(Submitter supplied) Berberine is a natural isoquinoline alkaloid found in Chinese medicinal herbs which is active against a variety of microbial infections. To examine the potential effects of berberine on Shigella flexneri, a whole-genome DNA microarray was constructed and transcriptome analysis of the cellular responses of S.flexneri when exposed to Berberine Chloride (BC) was performed.

Organism:

Shigella flexneri

Type:

Expression profiling by array

Platform:

GPL5068

3 Samples

Download data: GPR

(Submitter supplied) Using comparative genomic hybridization we examined the genome content of 30 isolates of E. coli and Shigella to determine the relative location of E. coli isolates from the human neobladder

Organism:

Shigella boydii; Escherichia coli; Shigella flexneri; Shigella; Shigella dysenteriae; Shigella sonnei

Type:

Genome variation profiling by array

Platform:

GPL13175

30 Samples

Download data: CEL

(Submitter supplied) Investigation of whole genome gene expression to identify overlooked sRNAs and sORFs. Background The completion of numerous genome sequences has introduced an era of whole-genome study. However, many real genes, including small RNAs (sRNAs) and small ORFs (sORFs), are missed in genome annotation. In order to improve genome annotation, we sought to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery or shigellosis. more...

Organism:

Shigella flexneri 2a str. 301

Type:

Expression profiling by genome tiling array

Platform:

GPL10653

15 Samples

Download data: PAIR