GEO DataSets

(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) Alveolar macrophages (AMs) are major targets of Mycobacterium tuberculosis (Mtb) infection, critical during the progression of active tuberculosis (TB). The complex immunopathology of TB generates diverse microenvironments in the lung, which shape immune responses by AMs. In the current study, we perform whole genome microarray transcriptional profiling on RNA isolated from AMs from TB patients (AMsTB) compared to AMs from control subjects (AMsCT) using bronchoalveolar lavage (BAL). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

7 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) 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) Whole-genome expression profiling on a cohort of TB patients. Tuberculosis patients above 15 years of age were recruited from an outpatient tuberculosis clinic in central Jakarta (Indonesia). Randomly selected control subjects with the same sex and age (+/-10%) were recruited from neighboring households, with first degree relatives excluded.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6883

71 Samples

Download data: TXT

(Submitter supplied) We report a study about differentially expressed small non-coding RNAs in the blood of humans harboring a latent (LTBI) or active tuberculosis (TB) infection in comparison with exposed controls (ExC) and treated LTBI (LTBItt). All non-TB subjects enrolled in this study were recent close contacts (rCt) of a newly diagnosed contagious TB cases enrolled in Rio de Janeiro, Brazil. The detailed methodology is described below. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

49 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to measure the immune response of alveolar macrophages (AMs) from mice lacking Nrf2 in LysM- or CD11c-expressing cells to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

12 Samples

Download data: TSV

(Submitter supplied) The aim of this study was to measure the immune response of alveolar macrophages (AMs) to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing. To determine the effect of the transcription factor Nrf2 on this response we also measured the transcriptional profiles of AMs from mice lacking Nrf2.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

54 Samples

Download data: TSV

(Submitter supplied) We present an infection study with pathogenic and non-pathogenic mycobacterial strains that have vastly different characteristics. The early/late host response to infection with these detergent-free cultured strains will be analysed through Ampliseq and further validated through qPCR in an attempt to provide information on the subtleties which may ultimately contribute to the virulent phenotype. Proceeding to the next objective of the study is to knock-down (siRNA)/knock-up (saRNA) selected differentially expressed mRNA to study their role in the intracellular survival of M. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

84 Samples

Download data: TXT, XLS

(Submitter supplied) Macrophages play an essential role in the early immune response to Mycobacterium tuberculosis and are the cell type preferentially infected in vivo. Primary macrophages and macrophage-like cell lines are commonly used as infection models, although the physiological relevance of cell lines, particularly for host-pathogen interaction studies, is debatable. Here we use high-throughput RNA-sequencing to analyse transcriptome dynamics of two macrophage models in response to M. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

36 Samples

Download data: TXT

(Submitter supplied) Understanding the mechanisms of host macrophage responses to Mycobacterium tuberculosis (M.tb.) is essential for uncovering potential avenues of intervention to boost host resistance to infection. Macrophage transcriptome profiling revealed M.tb. infection strongly induced expression of several enzymes controlling tryptophan (Trp) catabolism. This included indole 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO2), which catalyze the rate-limiting step in the kynurenine pathway, producing ligands for the aryl hydrocarbon receptor (AHR). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

8 Samples

Download data: CEL, XLSX

(Submitter supplied) Mycobacterium tuberculosis (M. tb), the cause of tuberculosis (TB), utilizes the blood circulation to spread systemically and establish infection, and the risk of developing active TB (pulmonary and extrapulmonary) is significantly increased in individuals infected with human immunodeficiency virus (HIV). In this work, we have used DNA microarray analysis to investigate the transcriptome of M. tb replicating in human whole blood from both HIV-negative and HIV-positive donors compared to M. more...

Organism:

Mycobacterium tuberculosis H37Rv; Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL4057

24 Samples

Download data: GPR

(Submitter supplied) Infection with Mycobacterium tuberculosis (M. tb) is initiated when an aerosol droplet carrying a few bacilli is inhaled into an alveolus. Alveolar epithelial cells (AEC) (type II and type I) are among the first cells encountered by the infecting bacteria and greatly outnumber macrophages in the alveolus. M. tb replicates dramatically (>20,000 fold) in a “non-migrating” compartment in the lung prior to the development of the cell-mediated immune response in aerosol-infected mice (Wolf AJ, 2008). more...

Organism:

Mycobacterium tuberculosis; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4057

6 Samples

Download data: GPR

(Submitter supplied) We examined the microRNA profiles of THP-1 macrophages upon the MTB infection of (1) Beijing/W and non-Beijing/W clinical strains, and (2) susceptible and multidrug-resistant (MDR-) MTB strains.

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL19763

14 Samples

Download data: TXT

(Submitter supplied) the microRNA profiles of the host macrophages were studied by microarray in a small cohort with active MTB disease, latent infection (LTBI), and from healthy controls.

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL19763

10 Samples

Download data: TXT

(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) Mycobacterial transcripts were identified in exosomes released from M.tb infected RAW264.7 macrophages that were not present in uninfected exosomes suggesting export of mycobacterial RNA via exosomes Mycobacterial RNA was used as positive control and RNA from exosomes released from uninfected macrophages was used as negative control

Organism:

Mycobacterium tuberculosis H37Rv; Mycobacterium tuberculosis

Type:

Expression profiling by array

Platform:

GPL18228

4 Samples

Download data: PAIR

(Submitter supplied) Investigation to study mRNA transcripts present in exosomes from M.tb infected cells and how they compare to those derived from uninfected cells. Transcripts were also studied in donor macrophages as controls The gene expression study identified unique transcripts as well as differentially expressed transcripts present in exosomes released from infected macrophages

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10572

12 Samples

Download data: PAIR, TXT

(Submitter supplied) Mycobacterium tuberculosis (Mtb) infects alveolar macrophages (AMs) causing pulmonary tuberculosis (PTB), the more frequent form of the disease. Less frequently, Mtb disseminates to many other organs and tissues resulting in different extrapulmonary forms of TB. Nevertheless, very few studies have addressed the global mRNA response of human AMs, in particular from humans with the active form of the disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

43 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL15520

52 Samples

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