GEO DataSets

(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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(Submitter supplied) Mycobacterium abscessus is an emerging pathogen causing pulmonary infections in those with inflammatory lung disorders, such as Cystic Fibrosis (CF), and is associated with the highest fatality rate among rapidly growing mycobacteria (RGM). Phenotypically, MAB manifests as either a Smooth (MAB-S) or a Rough (MAB-R) morphotype, which differ in their levels of cell wall glycopeptidolipids (GPLs) and in their pathogenicity in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL15520

27 Samples

Download data: XLS

(Submitter supplied) Mycobacterium abscessus is an emerging pathogen causing pulmonary infections in those with inflammatory lung disorders, such as Cystic Fibrosis (CF), and is associated with the highest fatality rate among rapidly growing mycobacteria (RGM). Phenotypically, MAB manifests as either a Smooth (MAB-S) or a Rough (MAB-R) morphotype, which differ in their levels of cell wall glycopeptidolipids (GPLs) and in their pathogenicity in vivo. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15520 GPL11154

25 Samples

Download data: XLS

(Submitter supplied) In this study, we were interested to get deeper insights into the molecular mechanisms that govern the formation and selection of the different colony morphologies in Mycobacterium abscessus strains, including the potential reversibility of the rough (R) phenotype into a smooth (S) phenotype. We used next generation sequencing (NGS) and micro-array / RNAseq approaches to determine the genome sequences and transcriptomic profiles of three isogenic S/R strain couples of M. more...

Organism:

Mycobacteroides abscessus

Type:

Expression profiling by array

Platform:

GPL15573

3 Samples

Download data: GPR, TXT

(Submitter supplied) RNA sequencing (RNA-seq) of Mycobacterium abscessus in four infection-relevant culture conditions: hypoxic stress, artificial sputum medium, kanamycin-treated medium, and erythromycin-treated medium.

Organism:

Mycobacteroides abscessus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21540

18 Samples

Download data: XLS

(Submitter supplied) The objective of this study is to develop an integrated map for the M. abscessus ATCC19977 organism. Among the data types contributing to the development of this map are next-generation RNA-sequencing, differential RNA-sequencing, ribosome profiling, and mass spectrometry.

Organism:

Mycobacteroides abscessus ATCC 19977

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20911 GPL20910

6 Samples

Download data: BED, TXT

(Submitter supplied) The initial interactions between a host cell and a pathogen can dictate disease outcomes and are important targets for host-directed therapies. Mycobacterium abscessus (Mab) is a highly antibiotic resistant, rapidly growing non-tuberculous mycobacterium that infects patients with chronic lung diseases, like cystic fibrosis. Mab can infect host immune cells, such as macrophages, which contribute to its pathogenesis. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL19057

6 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

36 Samples

Download data

(Submitter supplied) Bmdm cells were differentiated for 10 days and harvested and culture in six well plate followed by transfection with Batf2 ShRNA. Media was replanished in every two days and on 10th day cells were stimulated with IFNg for 4 hrs. Total RNA was obtain after 4 hrs of stimulation.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(Submitter supplied) Bmdm cells were differentiated for 10 days and harvested and culture in six well plate followed by cytokine stimulation total RNA was harvested at 2, 4, 6, 24 hrs

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

24 Samples

Download data: TXT

(Submitter supplied) Mice were challneged with Mycobacterium abscessus cell wall particles intra- tracheally or saline. Lung was harvested after 3 weeks. RNA extracted from lungs and RNASeq was performed to identify differentially expressed genes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

7 Samples

Download data: TXT

(Submitter supplied) Bronchial Epithelial cells were exposed to microparticles generated from mycobacterium abscessus MAB cell wall per an in-house protocol. Control group was exposed to saline. Differentially expressed genes related to MAB cell wall particles were determined.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) Chlamydia trachomatis is the most common sexually transmitted infection and the bacterial agent of trachoma globally. C. trachomatis undergoes a biphasic developmental cycle involving an infectious elementary body and a replicative reticulate body. Little is currently known about the expression of host cell mRNAs, lncRNAs, and miRNAs at different stages of C. trachomatis development. Here, we performed RNA-seq and miR-seq on HeLa cells infected with C. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL23227

20 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) 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) 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

(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) Novel high-throughput deep sequencing technology has dramatically changed the way that the functional complexity of transcriptomes can be studied. Here we report on the first use of this technology to gain insight into the wide range of transcriptional alterations that are associated with an infectious disease process. Using Solexa/Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing method, we investigated mycobacterium-induced transcriptome changes in a model vertebrate species, the zebrafish. more...

Organism:

Danio rerio

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL7735 GPL9319

8 Samples

Download data: XML

(Submitter supplied) We focused on how Mycobacterium avium subsp. paratuberculosis influences the subsequent host response to investigate the host immunopathology accompanying the host anti-mycobacterial immune response during Mycobacterium avium subsp. paratuberculosis infection in spleen of mice.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

12 Samples

Download data: TXT

(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