GEO DataSets

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:

Serratia marcescens; Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33401 GPL30015 GPL34033

6 Samples

Download data: MTX, TSV

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:

Lactiplantibacillus plantarum; Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33401 GPL30015 GPL34033

24 Samples

Download data: TXT

(Submitter supplied) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...

Organism:

Citrobacter rodentium; Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae; Salmonella enterica; Serratia marcescens

Type:

Expression profiling by high throughput sequencing

6 related Platforms

64 Samples

Download data: TXT

(Submitter supplied) Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are under characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. more...

Organism:

Cellvibrio japonicus; Chitinophaga pinensis; Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34520 GPL34518 GPL34519

48 Samples

Download data: CSV, XLSX

(Submitter supplied) Host-microbe interactions are virtually bidirectional, benefiting both the host and microbial sides. It is becoming increasingly recognized the influence of the microbe on many aspects of host physiology and diseases, but whether/how the host affects their symbionts is poorly characterized. Here, we reported that the host acts as a critical factor to shape the lifestyle of their symbionts in the Drosophila and bacteria model system. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33401

10 Samples

Download data: TSV

(Submitter supplied) Host-microbe interactions are virtually bidirectional, benefiting both the host and microbial sides. It is becoming increasingly recognized the influence of the microbe on many aspects of host physiology and diseases, but whether/how the host affects their symbionts is poorly characterized. Here, we reported that the host acts as a critical factor to shape the lifestyle of their symbionts in the Drosophila and bacteria model system. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33401

9 Samples

Download data: TXT

(Submitter supplied) To explore the role of indole-3-acetic acid (IAA) as signalling molecule in plant-associated bacteria we analyzed the whole transcriptome of S. plymuthica A153 wild type and its Δipdc mutant in vitro

Organism:

Serratia plymuthica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33188

6 Samples

Download data: TXT

(Submitter supplied) In order to identify mRNA and sRNAs associated with the RNA-binding protein Hfq in Serratia marcescens strain Db10, Hfq-bound RNA was immunoprecipitated from a strain encoding an Hfq-3FLAG fusion protein at the normal location and sequenced, in parallel with the wild type strain (no fusion) as negative control. Additionally global transcriptional start site mapping was performed on total RNA, with or without TEX treatment, isolated from wild type Serratia marcescens. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21500

4 Samples

Download data: WIG

(Submitter supplied) Serratia marcescens, a member of the order Enterobacterales, is adept at colonizing healthcare environments and an important cause of invasive infections. Antibiotic resistance is a daunting problem in S. marcescens because in addition to plasmid-mediated mechanisms, most isolates have considerable intrinsic resistance to multiple antibiotic classes. To discover endogenous modifiers of antibiotic susceptibility in S. more...

Organism:

Serratia marcescens subsp. marcescens ATCC 13880

Type:

Other

Platform:

GPL29934

5 Samples

Download data: XLSX

(Submitter supplied) The GumB protein is an IgaA-family member that negatively regulates the Rcs stress response system in the bacterium Serratia marcescens. Mutation of the gumB gene results in increased RCs system activity of numerous genes including those involved in flagellar based motility and capsular polysaccharide formation.

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28573

6 Samples

Download data: TXT

(Submitter supplied) We report the application of transcriptome sequencing technology for high-throughput profiling of Serratia marcescens for producing prodigiosin. By obtaining over 163 million bases of sequence from Serratia marcescens genome DNA, we generated transcriptome -state maps of Serratia marcescens 12h cells, 24h cells, and 36h cells at 30C and 37C,respectively. We explored the mechanism of S. marcescens response temperature regulation at the transcription level through transcriptome sequencing technology. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28109

12 Samples

Download data: TXT

(Submitter supplied) RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and SK8-37. S. marcescens JNB5-1 and SK8-37 cells were grown in LB medium for 10 h before harvesting. The collected cells were then treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis. For annotation, the genome of S. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26806

2 Samples

Download data: XLSX

(Submitter supplied) Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28109

4 Samples

Download data: XLSX

(Submitter supplied) RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and SK68. S. marcescens JNB5-1 and SK68 cells were grown in LB medium for 4 h before harvesting. The collected cells were then treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis. For annotation, the genome of S. marcescens WW4 (NC_020211.1) was used as reference. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26806

2 Samples

Download data: TXT

(Submitter supplied) The acid tolerance of industrial strains is a significant challenge in the fermentation process. The bacterium Serratia marcescens is part of the Enterobacteriaceae family of eubacteria, which is a potential industrial microorganism. However, the molecular mechanism behind S. marcescens acid resistance is not properly understood. In this study, we screened for novel regulators that respond to acidic conditions by a Tn5G transposon insertion mutagenesis of S. more...

Organism:

Serratia marcescens WW4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27450

2 Samples

Download data: TXT

(Submitter supplied) RNAseq analysis was performed to evaluate gene expression differences between strains JNB5-1 and ZK66. S. marcescens JNB5-1 and ZK66 cells were grown in LB medium for 12 h before harvesting. The collected cells were then treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis. For annotation, the genome of S. marcescens WW4 (NC_020211.1) was used as reference. A total of 24048918 reads matched to the referenced genome in the sample of JNB5-1, and 24569696 reads in the sample of ZK66. The differentially expressed genes (DEGs) were determined between strains JNB5-1 and ZK66 with the standards of false discovery rate (FDR) ≤ 0.05, fold change |log2Ratio|≥1. Transcriptome data showed that expression of 641 genes were upregulated while 784 genes were down regulated by at least 2-fold when comparing the metR mutant strain ZK66 to its parent strain JNB5-1. Based on the annotation of KEGG_B_class, the up-regulated and down-regulated genes were classified into 30 and 27 major cellular processes, respectively. The transcriptome data indicated that MetR may regulate a variety of cellular processes in S. marcescens, including prodigiosin synthesis, and cell motility.

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26806

2 Samples

Download data: TXT

(Submitter supplied) Results from previous experiments indicated that the Gram-negative a-proteobacterium Serratia liquefaciens strain ATCC 27592 was capable of growth under low temperature (0°C), low pressure (0.7 kPa), and anoxic, CO2-dominated atmosphere--conditions intended to simulate the near-subsurface environment of Mars (Schuerger A.C. et al., Astrobiology 13: 115-131, 2013). To probe the response of its transcriptome to this extreme environment, S. more...

Organism:

Serratia liquefaciens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25602

12 Samples

Download data: CSV, TXT

(Submitter supplied) The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. more...

Organism:

Serratia sp. BW106

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22269

6 Samples

Download data: XLSX

(Submitter supplied) Global amphibian declines and extinction events are currently occurring at an unprecedented rate. While various factors are influencing these declines, one factor that is readily identifiable is disease. Specifically, the fungal pathogen Batrachochytrium dendrobatidis is thought to play a major role in amphibian declines in tropical and neotropical regions of the globe. While the effects of this chytrid fungus have been shown to be devastating, certain individuals and relict populations have shown resistance. more...

Organism:

Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22119

6 Samples

Download data: TXT

(Submitter supplied) The RNA-seq technique aims to identify genes that are differently expressed in low nitrogen (2mM (NH4)2SO4) and high nitrogen (10mM (NH4)2SO4) conditions.

Organism:

Serratia sp. ZM

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20923

2 Samples

Download data: RPKM