GEO DataSets

(Submitter supplied) Scavenger receptors on the cell surface of macrophages play an important role in host defence through their ability to bind microbial ligands and induce phagocytosis. Concurrently, signal transduction pathways are initiated that aid in defence mechanisms against the invading microbe. Here we report on the function of scavenger receptor Marco (macrophage receptor with collagenous structure) during infection of zebrafish embryos with Mycobacterium marinum, a close relative of Mycobacterium tuberculosis. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TSV

(Submitter supplied) We use the Tlr2 mutant of zebrafish embryos model to study the transcriptome response to Mycobacterium marinum infection. We injected M.marinum into the caudal vein at 28 hours post fertilization and took samples at 4 days post infection.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

12 Samples

Download data: XLSX

(Submitter supplied) Both embryonic and adult zebrafish Mycobacterium marinum infection studies have contributed to our knowledge of the development and function of tuberculous granulomas, which are typical for mycobacterial pathogenesis. In this review we discuss how transcriptome profiling studies have helped to characterize this infection process and we include new RNA sequencing (RNA-Seq) data that reveals three main phases in the host response to M. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

72 Samples

Download data: TSV

(Submitter supplied) Zebrafish Mycobacterium marinum infection has been widely used to model human tuberculosis because these two diseases share common features, e.g. latency, granuloma formation and reactivation. Here we infected adult zebrafish with a low dose of M. marinum, which usually leads to a chronic infection. At 14 days post infection we performed microarray analysis to characterize the immune response against this infection. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

5 Samples

Download data: TXT

(Submitter supplied) Pathogenic mycobacteria have the ability to survive within macrophages and persist inside granulomas composed of host immune cells. The complex host-pathogen interactions that determine the outcome of a mycobacterial infection process result in marked alterations of the host gene expression profile. Here we used the zebrafish model to investigate the specificity of the host response to infections with two mycobacterium strains that give distinct disease outcomes: an acute disease with early lethality or a chronic disease with granuloma formation, caused by Mycobacterium marinum strains Mma 20 and E11, respectively. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

39 Samples

Download data: TXT, XML

(Submitter supplied) Macrophage expressed gene 1 (MPEG1) encodes an evolutionary conserved protein with a predicted Membrane Attack Complex/Perforin domain associated with host defence against invading pathogens. In vertebrates, MPEG1 is an integral membrane protein of macrophages, but how it contributes to the macrophage defence mechanisms remains unknown. Zebrafish have three copies of MPEG1, two of which (mpeg1 and mpeg1.2) are expressed in macrophages whereas the third could be a pseudogene. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

12 Samples

Download data: TSV

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

Organism:

Danio rerio

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL15180

16 Samples

Download data: TSV, TXT

(Submitter supplied) MyD88 is an adaptor protein in Toll-like receptor and interleukin 1 receptor mediated signaling pathways that plays an essential role in activation of immune responses following pathogen recognition. We investigate that role in the zebrafish embryo model by using a zebrafish mutant line that contains a premature stop condon in the gene encoding MyD88, leading to a truncated protein that lacks domains important for its normal function. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

4 Samples

Download data: TSV

(Submitter supplied) To gain additional insight into the role of MARCO in dendritic cell activation and function, we profiled transcriptomes of mouse splenic dendritic cells obtained from MARCO deficient mice and their wild type counterparts under resting and activating conditions.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5631

Platform:

GPL11180

4 Samples

Download data: CEL

Analysis of spleen dendritic cells (DCs) isolated from macrophage receptor with collagenous structure (MARCO)-knockout animals and cultured in media containing TLR agonist LPS. MARCO is part of the innate antimicrobial immune system. Results provide insight into the role of MARCO in activated DCs.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation, 2 protocol sets

Platform:

GPL11180

Series:

GSE55068

4 Samples

Download data: CEL

(Submitter supplied) Deficiency in the protein-tyrosine phosphatase SHP1/PTPN6 is linked with hematological malignancies and chronic inflammatory diseases. Here we exploited the embryonic and larval stages of zebrafish as an animal model to study ptpn6 function in the sole context of innate immunity. We show that ptpn6 knockdown induces a spontaneous inflammation-associated phenotype at the late larval stage, which was microbe-independent and enhanced instead of suppressed by glucocorticoids. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL13390

12 Samples

Download data: TXT

(Submitter supplied) Salmonella enterica serovar Typhimurium (S. typhimurium) bacteria cause an inflammatory and lethal infection in zebrafish embryos. To characterize the embryonic innate host response at the transcriptome level, we have extended and validated previous microarray data by Illumina next-generation sequencing analysis. Comparison of tag-based sequencing (DGE or Tag-Seq) with full transcript sequencing (RNA-Seq) showed a strong correlation of sequence read counts per transcript and an overlap of 241 transcripts differentially expressed in response to infection. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

Download data: TXT

(Submitter supplied) Mycobacterium marinum infection in zebrafish (Danio rerio) has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole-genome level transcriptome analysis. In addition, we carried out a medium-scale forward genetic screen to identify genes underlying defense mechanisms against M. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

4 Samples

Download data: TSV

(Submitter supplied) Mycobacterium marinum infection in zebrafish (Danio rerio) has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole-genome level transcriptome analysis. As expected based on the literature, our results showed the induction of genes coding proteins associated to immune signaling, cell migration and acute phase response indicating that the immune response to M. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23085

8 Samples

Download data: TSV

(Submitter supplied) Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found substantial differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

12 Samples

Download data: XLSX

(Submitter supplied) The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages, we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TSV

(Submitter supplied) Transcriptional profiling of the zebrafish embryonic host response to a systemic bacterial infection with Salmonella typhimurium (strain SL1027); comparison between traf6 knock-down and control morpholino treated embryos.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9319

4 Samples

Download data: SAM, TXT

(Submitter supplied) Transcriptional profiling of the zebrafish embryonic host response to a systemic bacterial infection with Salmonella typhimurium (strain SL1027); comparison between traf6 knock-down and control morpholino treated embryos.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL10042

24 Samples

Download data: TXT

(Submitter supplied) The mechanisms that govern the neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilize an innovative binary approach in zebrafish to perform in depth profiling of the initial response of neutrophils to Mycobacterium marinum, by in vivo biotinylation of neutrophil nuclei and subsequent rapid isolation directly from the in vivo context. RNA-seq and differential expression analysis of the neutrophil nuclear transcriptome reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, wu:fb15h11 (NLRC3 ortholog) and il1β. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

6 Samples

Download data: TXT

(Submitter supplied) DNA Damage Regulated Autophagy Modulator 1 (DRAM1) is a stress-inducible regulator of autophagy and cell death. DRAM1 has been implicated in cancer, myocardial infarction, and infectious diseases, but the molecular and cellular functions of this transmembrane protein remain poorly understood. Previously, we have proposed DRAM1 as a host resistance factor for tuberculosis (TB) and a potential target for host-directed anti-infective therapies. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

15 Samples

Download data: TSV