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Items: 1 to 20 of 134182

1.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Type:
Other
4 related Platforms
279 Samples
Download data
Series
Accession:
GSE264519
ID:
200264519
2.

TnpB homologs exapted from transposons are RNA-guided transcription factors

(Submitter supplied) Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. more...
Organism:
Escherichia coli; Enterobacter sp. BIDMC93; Enterobacter cloacae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms
51 Samples
Download data: BED, BW, XLSX
Series
Accession:
GSE245749
ID:
200245749
3.

RNA sequencing of bacterial samples under salt stress [CL3]

(Submitter supplied) This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
Organism:
Bacillus sp. (in: firmicutes)
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34384
4 Samples
Download data: TXT
Series
Accession:
GSE263918
ID:
200263918
4.

RNA sequencing of bacterial samples under salt stress [CL2]

(Submitter supplied) This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
Organism:
Vibrio natriegens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34383
4 Samples
Download data: TXT
Series
Accession:
GSE263917
ID:
200263917
5.

RNA sequencing of bacterial samples

(Submitter supplied) This study aimed to investigate the survival of an environmental isolate under salt stress and to identify the various genes involved in stress protection following RNA sequencing analysis. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to salt stress.
Organism:
Priestia megaterium
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34380
4 Samples
Download data: TXT
Series
Accession:
GSE263823
ID:
200263823
6.

Desiccation induces varied responses within a soil bacterial genus

(Submitter supplied) Nine Curtobacterium strains (three from three clades) were subjected to a lab desiccation experiment with no access to moisture or nutrients to compare between clades. RNA was extracted at days 0, 1, and 32 and sequenced
Organism:
Curtobacterium
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33356
81 Samples
Download data: CSV, SF
Series
Accession:
GSE230266
ID:
200230266
7.

The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation

(Submitter supplied) Mycobacterium avium subsp. paratuberculosis (MAP) carries MAP3773c, a putative metal regulator, on its genome which is absent in other mycobacteria. Homologues of this gene in enterobacteria have roles in global iron regulation and homeostasis. The role of MAP3773c in regulating intracellular iron in MAP is poorly understood. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis, sugar metabolism and N-acetyltransferase enhanced intracellular survival genes were downregulated at 30 minutes post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, arginine and proline metabolism, PPE, PE family and mammalian cell entry (MCE) genes were upregulated at that same time point. more...
Organism:
Mycobacterium avium subsp. paratuberculosis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33823
20 Samples
Download data: TXT
Series
Accession:
GSE244734
ID:
200244734
8.

Prophage-encoded methyltransferase upregulates virulence to drive adaptation in an outbreak of community-acquired methicillin-resistant Staphylococcus aureus [Harm analysis]

(Submitter supplied) To determine the effects of phage m⏀11 on gene expression in USA300 (LAC*)
Organism:
Staphylococcus aureus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27158
4 Samples
Download data: TXT
Series
Accession:
GSE255351
ID:
200255351
9.

Prophage-encoded methyltransferase upregulates virulence to drive adaptation in an outbreak of community-acquired methicillin-resistant Staphylococcus aureus

(Submitter supplied) To determine the effects of phage adenine methyltransferase (pamA) on gene expression in WT USA300 (LAC*)
Organism:
Staphylococcus aureus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27158
5 Samples
Download data: TSV
Series
Accession:
GSE252862
ID:
200252862
10.

Robust Host Engineering: Enhancing Escherichia coli´s Abiotic Stress Resistance through Ornithine Lipid Membrane Modification

(Submitter supplied) Transcriptome analysis revealed that strains had differentially expressed stress and membrane-related genes compared to the control strain
Organism:
Escherichia coli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25368
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE233657
ID:
200233657
11.

Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli

(Submitter supplied) Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g. in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e. more...
Organism:
Escherichia coli BW25113; Escherichia coli str. K-12 substr. MG1655
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL32899 GPL34252
12 Samples
Download data: XLSX
Series
Accession:
GSE260455
ID:
200260455
12.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq9 (LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Type:
Other
4 related Platforms
48 Samples
Download data: CSV
Series
Accession:
GSE262848
ID:
200262848
13.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq13 (Typhi and Paratyphi A infection of THP-1 human macrophages)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Type:
Other
Platforms:
GPL34286 GPL34287
9 Samples
Download data: CSV
Series
Accession:
GSE262769
ID:
200262769
14.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq12 (Typhimurium THP-1 infections)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Type:
Other
Platforms:
GPL34285 GPL34288
12 Samples
Download data: CSV
Series
Accession:
GSE262768
ID:
200262768
15.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq6 (anaerobic LB, GMM, zinc, Nmedia, protamine- second set)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Type:
Other
4 related Platforms
28 Samples
Download data: CSV
Series
Accession:
GSE261873
ID:
200261873
16.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq5 (anaerobic LB, GMM, zinc, Nmedia, protamine)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Type:
Other
4 related Platforms
24 Samples
Download data: CSV
Series
Accession:
GSE261867
ID:
200261867
17.

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))

(Submitter supplied) 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. more...
Organism:
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; Salmonella enterica subsp. enterica serovar Typhi str. Ty2
Type:
Other
4 related Platforms
40 Samples
Download data: CSV
Series
Accession:
GSE261860
ID:
200261860
18.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq3 (LB, ceftriaxone, ciprofloxacin, azithromycin)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
Type:
Other
4 related Platforms
40 Samples
Download data: CSV
Series
Accession:
GSE261757
ID:
200261757
19.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq2 (Bile, iron restriction, osmotic pressure, heat)

(Submitter supplied) 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. more...
Organism:
Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Type:
Other
4 related Platforms
40 Samples
Download data: CSV
Series
Accession:
GSE261749
ID:
200261749
20.

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq1 (NonSPI2, InSPI2, InSPI2Mg, M9glucose)

(Submitter supplied) 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. more...
Organism:
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
Type:
Other
4 related Platforms
38 Samples
Download data: CSV
Series
Accession:
GSE261214
ID:
200261214
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