GEO DataSets

(Submitter supplied) Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15749

78 Samples

Download data: TXT, XLSX

(Submitter supplied) Whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome (5-methylcytosine). The methylomes of bAM infected with M. bovis (n = 8) were compared to those of non-infected control bAM (n = 8) at 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed between control and infected bAM. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation = 33–66%). more...

Organism:

Bos taurus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19172

16 Samples

Download data: TXT

(Submitter supplied) Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15750

14 Samples

Download data: TXT, XLSX

(Submitter supplied) Purpose: The goal of this RNA-seq study was to profile changes in miRNA expression in bovine alveolar macrophages isolated from Holstein-Friesian and challenged with M. bovis over a 48 hour time course. Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major infectious disease problem for global agriculture, resulting in losses of billions of Euros annually. The bacterium spreads via an airborne route and is taken up by alveolar macrophages in the lung. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15749

88 Samples

Download data: TXT

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

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL23295 GPL19172

30 Samples

Download data: BW, TXT

(Submitter supplied) Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19172

8 Samples

Download data: TXT

(Submitter supplied) Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23295

8 Samples

Download data: TXT

(Submitter supplied) Massive reprogramming of the host alveolar macrophage transcriptome occurs during the initial stages of tuberculosis. In bovine tuberculosis, Mcobacterium bovis can persist and replicate within alveolar macrophages through varied mechanisms to subvert or exploit host immune responses ( REF). To determine how these transcriptional changes are regulated we performed ChIPseq analysis of H3K4 and H3K27 methylation, established histone tail markers associated with permissive and repressive chromatin states, respectively. more...

Organism:

Bos taurus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23295

14 Samples

Download data: BW

(Submitter supplied) Bovine tuberculosis (BTB) caused by Mycobacterium bovis continues to cause substantial losses to global agriculture and has significant repercussions for human health. The advent of high throughput genomics has facilitated large scale gene expression analyses that present a novel opportunity for revealing the molecular mechanisms underlying chronic mycobacterial infection. Using this approach, we have previously shown that innate immune genes in peripheral blood mononuclear cells (PBMC) from BTB-infected animals are repressed in vivo in the absence of exogenous stimulation. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL5751

36 Samples

Download data: GPR

(Submitter supplied) Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cells types to encounter M. bovis following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro challenge with M. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL2112

49 Samples

Download data: CEL

(Submitter supplied) Background: Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better understand the molecular mechanisms governing the host immune response to M. bovis infection. Furthermore, these studies may enable the identification of novel transcriptional markers of BTB that can augment current diagnostic tests and surveillance programmes. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL2112

16 Samples

Download data: CEL

(Submitter supplied) In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same PBL-extracted RNA

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15750

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Background: Bovine tuberculosis is an enduring disease of cattle that has significant repercussions for human health. The advent of high-throughput functional genomics technologies has facilitated large-scale analyses of the immune response to this disease that will ultimately lead to novel diagnostics and therapeutic targets. Analysis of mRNA abundance in peripheral blood mononuclear cells (PBMC) from six Mycobacterium bovis infected cattle and six non-infected controls was performed. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL5751

12 Samples

Download data: GPR

(Submitter supplied) Infection of cattle with Mycobacterium bovis causes severe financial hardship in many countries, in addition to presenting a health risk for humans. As an intracellular pathogen, M. bovis, adapted to survive and thrive within the intramacrophage environment. However, little is known about expression patterns in the macrophage, particularly in the bovine host. In this study, DNA microarray analysis was used to detect genes expressed in Holstein bovine macrophages derived from peripheral blood mononuclear cells infected during four hours with two Argentinean strains of M. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL2112

10 Samples

Download data: CEL

(Submitter supplied) Mycobacterium bovis (M. bovis) and Mycobacterium avium subspecies paratuberculosis (MAP) are important pathogens of cattle, causing bovine tuberculosis and Johne’s disease respectively. M. bovis and MAP infect residential macrophages in the lung and intestines respectively and subvert the macrophage biology to create a survival niche. To investigate this interaction we simultaneously studied the transcriptional response of bovine monocyte-derived macrophages to infection with two strains of M. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11153

80 Samples

Download data: TXT

(Submitter supplied) The definition of biomarkers correlating with disease progression could have impact on the rational design of novel diagnostic approaches for bovine tuberculosis in cattle. We have used the advantages of the murine model to identify promising candidates in the host transcriptome post-infection. RNA from BALB/c splenocytes and lung cells after aerogenic Mycobacterium bovis infection were with high-density microarrays to defining biomarkers of disease progression. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

25 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of this study is to explore the role of miRNAs in dairy cow response to E. coli and S. aureus, mastitis causing pathogens, is not well understood. Results: The global expression of miRNAs in bovine mammary epithelial cells (MAC-T cells) challenged with heat-inactivated Staphylococcus aureus (S. aureus) or Escherichia coli (E. coli) bacteria (treatments: 6, 12, 24 and 48 hr) and without challenge (control: 0, 6, 12, 24 and 48 hr) was profiled using next-generation-sequencing. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17875

13 Samples

Download data: TXT

(Submitter supplied) Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL17303

36 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression level changes in porcine alveolar macrophage response to co-infection of PRRSV and M. hyopneumoniae The results in this study will be further described in Bin li et al., 2013. BMC genomics.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL17577

24 Samples

Download data: PAIR

(Submitter supplied) In this study, we determined the miRNA expression profile of bovine alveolar macrophages, using next-generation sequencing strategy. On an Illumina HiSeq 2000 machine, we sequenced 8 miRNA libraries, prepared from small RNA fractions of alveolar macrophages isolated from 8 different healthy animals (Bos taurus). From the data, the potential novel miRNAs were predicted, and the expression levels of the known miRNAs were determined. more...

Organism:

Bos taurus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15749

8 Samples

Download data: TXT