GEO DataSets

(Submitter supplied) We used zebrafish embryos as an in vivo system to investigate the role of the microRNA-146 family (consisting of 2 members miR-146a and miR-146b) in the innate immune response to S. typhimurium infection. To determine the role of miR-146 microRNAs in the response to S. typhimurium infection we used Illumina RNA sequencing to compare the mRNA expression profiles of control embryos versus embryos with knockdown of miR-146a and miR-146b. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

8 Samples

Download data: TSV

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

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by array

Platforms:

GPL15403 GPL14875

17 Samples

Download data: TSV, TXT

(Submitter supplied) This study reports on infection-inducible miRNAs in zebrafish. Using a custom-designed microarray platform for miRNA expression we found that miRNAs of the miR-21, miR-29, and miR-146 families were commonly induced by infection of zebrafish embryos with Salmonella typhimurium and by infection of adult fish with Mycobacterium marinum.

Organism:

Danio rerio

Type:

Non-coding RNA profiling by array

Platform:

GPL15403

9 Samples

Download data: 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 array

Platform:

GPL10042

24 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) Characterization of the zebrafish embryonic host response to systemic bacterial infection with Salmonella typhimurium wild type strain (SL1027) and its isogenic LPS O-antigen mutant Ra (SF1592) by means of a time-resolved global expression analysis.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

36 Samples

Download data: XML

(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) 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:

GPL15180 GPL14875

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) 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11429

18 Samples

Download data

(Submitter supplied) Peripheral blood transcriptome is an important intermediate data source for investigation of the mechanism of Salmonella invasion, proliferation, and transmission but its development in pig is quite limited. We challenged four-week-old piglets (Duroc × Landrace × Yorkshire crossbred) with Salmonella enterica serovar Typhimurium LT2 and investigated the peripheral blood miRNA expression profile before treatment (d0) and at 2 days post inoculation (dpi) using deep sequencing technology.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11429

6 Samples

Download data: TXT

(Submitter supplied) Peripheral blood transcriptome is an important intermedia data source for investigation of the mechanism of Salmonella invasion, proliferation, and transmission but its development in pig is quite limited. We challenged four weeks old piglets (Duroc × Landrace × Yorkshire crossbred) with Salmonella enterica serovar Typhimurium LT2 and investigated the peripheral blood gene expression profile before treatment (d0) and at 2 and 7 day post inoculation (dpi) using deep sequencing technology.

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11429

12 Samples

Download data: TXT

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

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array; Expression profiling by array

Platforms:

GPL16045 GPL16044

19 Samples

Download data: GPR, TXT

(Submitter supplied) The host response to S.typhimurium infections in ileum was studied after infection of piglets. mRNA and miRNA expression studies were performed to identify interactions of miRNAs and regulated mRNAs in context of mammalian intestinal Salmonella infection using a piglet model.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL16045

9 Samples

Download data: GPR

(Submitter supplied) The host response to S.typhimurium infections in ileum was studied after infection of piglets. mRNA and miRNA expression studies were performed to identify interactions of miRNAs and regulated mRNAs in context of mammalian intestinal Salmonella infection using a piglet model.

Organism:

Sus scrofa

Type:

Non-coding RNA profiling by array

Platform:

GPL16044

10 Samples

Download data: TXT

(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