GEO DataSets

(Submitter supplied) Macrophages are immune cells inctributing to several kinds of diseases, and activation status of macrophages are considered to be regulated by several stimulations. To test the gene expression change in activated macrophages, human monocyte-derived macrophages were stimulated with alpha1-acid glycoprotein (AGP), anti-CD74 blocking antobody, anti-CD74-agonistic antibody. Macrophages infected with Micobacterium avium were also tested. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) Viromes of sour and sweet cherry trees in Hungarian germ line collections were surveyed using small RNA HTS as an unbiased method. RNA from leaf samples of different cultivars were purified and used to produce seven pools from which small RNA HTS libraries were prepared. The sequenced reads were analyzed using bioinformatic methods to revel the presence of viruses in the samples. Presence of the viruses were validated using RT-PCR.

Organism:

Prunus avium; Prunus cerasus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL33434 GPL23007

7 Samples

Download data: TXT

(Submitter supplied) Macrophages are immune cells inctributing to several kinds of diseases, and activation status of macrophages are considered to be regulated by several stimulations. To test the gene expression change in activated macrophages, human monocyte-derived macrophages were stimulated with alpha1-acid glycoprotein (AGP), anti-CD74 blocking antobody, anti-CD74-agonistic antibody. Macrophages infected with Micobacterium avium were also tested. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) The incidence of Mycobacterium avium complex (MAC)-induced pulmonary disease (PD) has been increasing in South Korea, posing considerable challenges in treatment. Treatment guidelines recommend initiating therapy after serial computed tomography (CT) monitoring. While drug treatment often improves outcomes in patients with the nodular bronchiectatic (NB) form, those with the fibrocavitary (FC) form may continue to experience persistence despite treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

42 Samples

Download data: XLSX

(Submitter supplied) Background: Johne’s disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne’s disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne’s disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne’s disease in dairy cattle. more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19172

16 Samples

Download data: CSV

(Submitter supplied) Mycobacterium avium subsp. paratuberculosis (MAP) carries MAP3773c, a putative metal regulator, on its genome which is absent in other mycobacteria. Homologues of this gene in enterobacteria have roles in global iron regulation and homeostasis. The role of MAP3773c in regulating intracellular iron in MAP is poorly understood. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis, sugar metabolism and N-acetyltransferase enhanced intracellular survival genes were downregulated at 30 minutes post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, arginine and proline metabolism, PPE, PE family and mammalian cell entry (MCE) genes were upregulated at that same time point. more...

Organism:

Mycobacterium avium subsp. paratuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33823

20 Samples

Download data: TXT

(Submitter supplied) Pseudomonas syringae pv. syringae 9644 (Pss9644) is a causal agent of bacterial cherry canker causing necrotic symptoms on leaves, fruits, gummosis and canker in woody tissues of sweet cherry (Prunus avium). To understand which virulent factor genes were expressed in vitro, Pss9644 was grown in rich media (King's B Broth) and minimum media (hrp-inducing minimum media). The latter mimics the in planta environment.

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 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; Other

Platform:

GPL20795

42 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) We performed scTCR-seq to investigate overall immune cell populations and distribution of MAC-PD patients, according to their clinical outcome.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

21 Samples

Download data: CSV

(Submitter supplied) We performed scRNA-seq to investigate overall immune cell populations and distribution of MAC-PD patients, according to their clinical outcome.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

21 Samples

Download data: MTX, TSV

(Submitter supplied) Mycobacterium avium complex (MAC), including Mycobacterium avium and Mycobacterium intracellulare (MI), accounts for a significant portion of nontuberculous mycobacterial lung disease affecting immunocompromised and lung structural disease patients. Adapting pathogens to a host-induced hostile environment is critical to establishing infection and persistence within the host. However, the cellular and molecular mechanisms of stress response for MAC still need to be elucidated. more...

Organism:

Mycobacterium intracellulare

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33797

9 Samples

Download data: TXT

(Submitter supplied) Mycobacterium avium complex (MAC) is a non-tuberculosis mycobacteria widely distributed throughout environment. Even though the MAC infection is currently increasing in old women and patients with affected immune system, comprehensive analysis of MAC-infected host cell transcriptome, in particular that of long non-coding RNAs (lncRNAs), has scarcely been reported. Using in vitro cultured primary mouse bone marrow-derived macrophages (BMDMs) and CAGE technology, we analyzed the transcriptional and kinetic landscape of macrophage genes, with focusing on lncRNAs, during MAC infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

32 Samples

Download data: TXT

(Submitter supplied) Background: Mycobacterium avium is an opportunistic pathogen that requires complex multidrug treatment. Macrolides, like clarithromycin, are the cornerstone of treatment, but even macrolide-based treatment regimens have suboptimal outcomes. Combining transcriptomic profiling of macrophages and mycobacteria in an in vitro infection model may increase our understanding of the host-pathogen interaction and the effect of antibiotic treatment. more...

Organism:

Mycobacterium avium subsp. hominissuis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32656

6 Samples

Download data: XLSX

(Submitter supplied) Background: Mycobacterium avium complex (MAC) bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and is comprised of a macrolide, a rifamycin and ethambutol; and in severe cases amikacin. Mechanisms of antibiotic tolerance remain mostly unknown. To elucidate these mechanisms, we studied the transcriptomic response to antibiotics and investigated the contribution of efflux and amikacin modification to susceptibility. more...

Organism:

Mycobacterium avium subsp. hominissuis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32656

36 Samples

Download data: XLSX

(Submitter supplied) Purpose: To evaluate whether methylation changes occuring upon M. avium infection correlate with transcriptional alterations in trained HSCs, we reisolated CD45.2 untrained vs. trained HSCs (LK CD150+CD48–) from transplanted mice one-month after M. avium challenge to generate bulk RNA-Seq libraries. We compared both libraries to a library from HSCs of WT donor mice following primary M. avium infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: CSV

(Submitter supplied) purpose: Chronic inflammation induced by Mycobacterium avium infection (timepoint= 1 month) results in transcriptomic changes within the HSC population subset upon bulk RNA-seq, particularly in pathways involved in the immune response, interferon gamma signaling (Th1 immune response) pathway, stat signaling, and antigen processing and presentation. We have also shown that chronic inflammation results in a myeloid differentiation bias of HSPCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: CLOUPE, CSV, H5, MTX, TSV, TXT

(Submitter supplied) To investigate the molecular mechanisms responsible for bone loss during mycobacterial infections

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27583

6 Samples

Download data: TXT

(Submitter supplied) Temperate perennial plants have to adapt their growth in order to survive over winter conditions and protect their tissues by entering into dormancy. The dormancy phenomenon is a complex process regulated by many factors, externals (photoperiod and temperature) or internals through the transport towards the buds. In order to better understand the molecular mechanisms involved in the regulation of dormancy, we conducted a transcriptomic analysis of flower buds from the late flowering sweet cherry cultivar 'Fertard' during dormancy, from October 2017 to March 2018.

Organism:

Prunus avium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33329

18 Samples

Download data: TXT

(Submitter supplied) Purpose: to identify the binding sites for BATF2 in HSCs during M. avium infection, we conducted CUT&RUN sequencing of the HSCs from infected WT mice using an anti-BATF2 antibody. We used an anti-IgG antibody as a control to exclude noise and nonspecific binding and an anti-H3K27ac to assess open chromatin Methods: 10,000-50,000 HSCs (CD45.1/CD45.2 KL CD150+ CD48-) into HBSS from1-month infected WT mice (n=10-12 per group). more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

7 Samples

Download data: XLSX

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

23 Samples

Download data: XLSX