GEO DataSets

(Submitter supplied) The overall objective of the study is to evaluate a bone marrow microfluidic system for its ability to predict expected hematopoietic liabilities of immunotherapeutics. The human bone marrow model consists of a zirconium oxide/hyaluronic acid scaffold, primary human stromal cells, and primary human CD34+ hematopoietic stem and progenitor cells. RNA sequencing was used to investigate changes in gene expression signatures of mesenchymal stromal cells when cultured on the ceramic scaffold, when cultured in a hematopoietic culture medium, and when cultured in the microfluidic system.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

11 Samples

Download data: TXT

(Submitter supplied) Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display vast metabolic and transcriptional diversity along with high recalcitrance to antibiotics and host immune defenses. Investigating the complex heterogeneity within biofilm has been hindered by the lack of a sensitive and high-throughput method to assess stochastic transcriptional activity and regulation between bacterial subpopulations, which requires single-cell resolution. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28116

2 Samples

Download data: TXT

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

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL28679 GPL25368 GPL29157

26 Samples

Download data

(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Streptococcus agalactiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29157

18 Samples

Download data: TXT

(Submitter supplied) Hepatocytes-like cells (HLC) derived from human induced pluripotent stem cells show great promise for cell-based liver therapies and disease modelling. However, their application is currently hindered by the low production yields of existing protocols. We aim to develop a bioprocess able to generate high numbers of HLC. We used stirred-tank bioreactors with a rational control of dissolved oxygen concentration (DO) for the optimization of HLC production as 3D aggregates. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

27 Samples

Download data: TXT

(Submitter supplied) Drugs and other xenobiotics are not only secreted/reabsorbed by the renal proximal tubule epithelial cells (RPTEC) but may also adversely impact kidney function. In vitro models that can afford prediction of toxic effects and model directional transport are in high demand in both drug and chemical safety; accordingly, active development of new models is underway. The objective of this study was to investigate physiological and transport function of various sources of human RPTECs under static and fluidic conditions. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

69 Samples

Download data: CSV

(Submitter supplied) Parkinson's disease (PD) is a neurodegenerative disease characterized by bradycardia, static tremor, rigidity and postural instability. At present, the current knowledge remains inadequate for the connection between the disease severity and peripheral immune response. In the present study, using single-cell RNA sequencing (scRNA-seq), we profiled peripheral blood mononuclear cells (PBMCs) from clinical cases, including 2 early PD, 2 advance PD and 2 matched controls, representing five major immune cell subsets: T cells (CD4+, CD8+), monocytes, B cells, natural killer (NK) cells and hematopoietic stem cells (HSCs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: MTX, TSV

(Submitter supplied) Lamellated corpuscles are rapidly adapting mechanoreceptors that detect transient touch and high-frequency vibration in many vertebrates. It the prevailing model, these properties are determined by outer core, which acts as a mechanical filter that limits static and low-frequency stimuli from reaching afferent terminal—the sole site of touch detection in corpuscles. Using focused ion beam scanning electron microscopy and single corpuscle electrophysiology, we determine the detailed architecture of corpuscular components and reveal their contribution to touch detection. more...

Organism:

Anas platyrhynchos

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28134

13 Samples

Download data: XLSX

(Submitter supplied) Colorectal cancer (CRC) tumors start as precancerous polyps on the inner lining of the colon or rectum, where they are exposed to the mechanics of colonic peristalsis. Our previous work leveraged a custom-built peristalsis bioreactor to demonstrate that colonic peristalsis led to cancer stem cell enrichment in colorectal cancer cells. However, this malignant mechanotransductive response was confined to select CRC lines that harbored an oncogenic mutation in the KRAS gene. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

18 Samples

Download data: CSV

(Submitter supplied) Membrane-less subcellular compartments such as cytoplasmic bodies, nuclear bodies, and paraspeckles play important roles in a variety of cellular functions. Although many of the techniques for identifying the components of cellular bodies were developed to address their function, no technique to comprehensively identify the components of these bodies in both static and dynamic states has been established. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

13 Samples

Download data: BW

(Submitter supplied) Asymptomatic colonization of the upper respiratory tract is a common trait of the two exclusive human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. In vivo models of pathogenic neisserial infections are heterologous systems that permit short-term persistence but do not fully recapitulate infections in humans. Studying Neisseria musculi (Nmus), an oral commensal, in laboratory mice allows investigation of Neisseria-host interactions that avoids host restriction barriers. more...

Organism:

Neisseria musculi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30638

6 Samples

Download data: XLSX

(Submitter supplied) Puumala orthohantavirus (PUUV) infection in humans can result in hemorrhagic fever with renal syndrome. Endothelial cells (ECs) are primarily infected with increased vascular permeability as a central aspect of pathogenesis. Historically, most studies included ECs cultured under static two-dimensional (2D) conditions, thereby not recapitulating the physiological environment due to their lack of flow and inherent pro-inflammatory state. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

18 Samples

Download data: TSV

(Submitter supplied) Cellular and molecular dynamics of human cells are constantly affected by gravity. Alteration of the gravitational force disturbs the cellular equilibrium, which might modify physiological and molecular characteristics. Nevertheless, biological responses of cancer cells to reduced gravitational force remains obscure. Here, we aimed to comprehend not only transcriptomic patterns but drug responses of colorectal cancer (CRC) under simulated microgravity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) Aims：To establish a novel model of mechanical loading-induced knee osteoarthritis (KOA) and explore its regulatory mechanisms through transcriptomics. Methods：Knee joints of Sprague-Dawley (SD) rats were mechanically loaded with 13 N, 20 N and 27 N for 2 or 4 weeks to construct mechanically-induced KOA model. Immunohistochemistry (IHC), quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, Safranin O/fast green staining, enzyme-linked immunosorbent assay (ELISA), micro-computed tomography (Micro-CT) and behavioral analysis were used to evaluate damage on the right knee joint. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

6 Samples

Download data: XLS

(Submitter supplied) Fluid shear stress (FSS) from blood flow sensed by vascular endothelial cells (ECs) determines vessel behavior but regulatory mechanisms are only partially understood. We used cell State Transition Assessment and Regulation (cSTAR), a powerful new computational method, to elucidate EC transcriptomic states under low shear stress (LSS), physiological shear stress (PSS), high shear stress (HSS), and oscillatory shear stress (OSS) that induce vessel inward remodeling, stabilization, outward remodeling or disease susceptibility, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

33 Samples

Download data: CSV

(Submitter supplied) Exposure to microgravity in low-Earth orbit (LEO) has been shown to affect human health. Post-flight brain imaging and studies of astronauts and mouse models suggest that microgravity may cause intracranial fluid shifts and possibly alter white and gray matter of the brain. To focus on the effects of microgravity on brain cells, we used induced pluripotent stem cells (iPSCs) to produce three-dimensional (3D) human neural organoids as models of the nervous system. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

42 Samples

Download data: TXT

(Submitter supplied) Biomaterial-based bone tissue engineering offers a promising prospect for the treatment of bone defects. In particular, the ability of biomaterials to regulate the immune microenvironment of the defect site is essential for effective bone regeneration. Electro-biomaterials have been confirmed to induce macrophage M2 polarization through metabolic pathways, thereby enhancing bone regeneration. Considering the central role of mitochondria in cellular metabolism and their ability to influence the function of neighboring cells through intercellular transfer, and inspired by the fact that tumor cells can uptake mitochondria from immune cells to generate energy, we hypothesize that the metabolic activation of immune cells by electro-materials can be transmitted to preosteoblasts through mitochondria to promote bone repair. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) As the limited arsenal of effective antifungals in clinical use is threatened by emerging resistance, the demand for new strategies to combat invasive fungi is urgent. One strategy to expand the therapeutic target space is to identify genes important for pathogen growth in host-relevant environments. Here, we leveraged a pooled functional genomic screening strategy to identify and characterize genes important for fitness of the human fungal pathogen Candida albicans in diverse conditions. more...

Organism:

Candida albicans

Type:

Other

Platforms:

GPL22403 GPL23041

114 Samples

Download data: CSV

(Submitter supplied) Liver regeneration starting from hepatocyte proliferation was reported to be correlated with blood flow changes after partial hepatectomy (PHx). However, the regulatory effects of flow-induced shear stress on initiating hepatocyte proliferation have not been elucidated. Thus, the isolated hepatocytes were exposed to shear stress to identify their transcriptome changes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

8 Samples

Download data: TXT

(Submitter supplied) Lung tissue-resident memory CD8+ T-cells (Trm) are critical for heterosubtypic immunity against influenza virus-(IAV)-reinfection. How these cells surveil the lung, respond to infection and interact with other cells remains unresolved. Here, we used mouse models to identify and enrich lung Trm in combination with intravital and static imaging to assess spatiotemporal dynamics of IAV-induced lung TRM before and after recall-infection. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: TXT