GEO DataSets

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL30173 GPL18573

79 Samples

Download data: BW

(Submitter supplied) The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

26 Samples

Download data: BW

(Submitter supplied) COVID-19 is characterized by systemic proinflammatory shifts with development of serious alterations in the functioning of the immune system. Investigations of the gene expression changes accompanying infection state provide insight towards understanding of the molecular and cellular processes depending on the sickness severity and virus variant. Severe Delta COVID-19 have been characterized by the appearance of the monocyte subset enriched for the proinflammatory gene expression signatures and shift of the ligand-receptor interactions. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL30173

39 Samples

Download data: BED, MTX, TSV

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL30173

21 Samples

Download data

(Submitter supplied) Atherosclerosis, which develops in the inner layer of arteries, is the major cause of myocardial infarction and stroke. Atherosclerotic plaques develop preferentially in arterial regions exposed to disturbed blood flow, such as vessel curvatures, bifurcations and branching points, where endothelial cells develop an inflammatory phenotype. How disturbed flow induces endothelial cell inflammation is incompletely understood. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

(Submitter supplied) Human Immunodeficiency Virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its lifecycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combination of ribosome profiling, disome sequencing and RNA sequencing. We show that HIV-1 mRNAs are efficiently translated at all stages of infection, despite evidence for a substantial decrease in translational efficiency of host genes that are implicated in host cell translation. more...

Organism:

Human immunodeficiency virus 1; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

32 Samples

Download data: BED, CSV, TXT

(Submitter supplied) Gene expression is controlled by dynamic localization of thousands of regulatory proteins to precise genomic regions. Understanding this cell-type specific process has been a longstanding goal yet remains challenging because DNA-protein mapping methods generally study one protein at a time. To address this, we developed ChIP-DIP (ChIP Done In Parallel) to generate genome-wide maps of hundreds of diverse regulatory proteins in a single experiment. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

4 related Platforms

10 Samples

Download data: BIGWIG, XLSX

(Submitter supplied) Microfluidic human skin equivalents (HSEs) were constructed by 3D printing and consisted of an endothelial lined vascular microchannel within a 3D dermal matrix embedded with fibroblasts. Keratinocytes were cultured on the surface to mimic the epidermis. Following exposure of the epidermis to lipopolysaccharide (LPS) and nigericin, human monocytes were injected into the vascular channel and migrated into the HSE. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

4 Samples

Download data: MTX, TSV

(Submitter supplied) Neural stem cell (NSC)-based therapies can exploit the inherent pathotropism of NSCs to deliver neurotrophic factors for cell replacement therapies and to stimulate endogenous neurogenesis to permanently repair damaged brain tissue after brain injury. Despite studies on the protective/restorative functions of NSCs and their extracellular vesicles (EVs), a major impediment to advancing this approach to late-stage preclinical studies and clinical practice has been the lack of molecular characterization of NSCs and NSC-EV cargo composition. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

4 Samples

Download data: CSV

(Submitter supplied) Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing of the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30173

3 Samples

Download data: CSV, H5, JSON, MTX, PNG, TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL18573

28 Samples

Download data

(Submitter supplied) The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. We applied selective ribosome profiling to further investigate the determinants of CCR4-NOT recruitment to ribosomes in mammalian cells. This revealed that specific arginine codons in the P-site are strong signals for ribosomal recruitment of human CNOT3, a CCR4-NOT subunit. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

24 Samples

Download data: XLSX

(Submitter supplied) RNAs undergo a complex choreography of metabolic processes that are regulated by thousands of RNA-associated proteins. Here we present a massively parallel RNA-linked CRISPR (ReLiC) platform to measure the responses of diverse RNA metabolic events to knockout of 2,092 human genes encoding all known RNA-associated proteins. ReLiC relies on a pooled, virus-free, serine recombinase-based strategy to integrate DNA libraries encoding Cas9, multiple sgRNAs, and barcoded reporters into a defined genomic locus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

16 Samples

Download data: TAB

(Submitter supplied) A critical aspect of the mechanism of SARS-CoV-2 infection is the protease-mediated activation of the viral spike (S) protein. The type II transmembrane serine protease TMPRSS2 is crucial for SARS-CoV-2 infection in lung epithelial Calu-3 cells and murine airways. However, the importance of TMPRSS2 needs to be re-examined because the ability to utilize TMPRSS2 is significantly reduced in the Omicron variants that spread globally. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

(Submitter supplied) N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. In this study, we reveal that m6A sites in the coding sequence (CDS) trigger CDS–m6A decay (CMD), a novel mRNA decay pathway that is distinct from previously reported m6A-dependent degradation mechanisms. Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors of m6A-mediated RNA decay. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

18 Samples

Download data: TXT

(Submitter supplied) To investigate the response mechanisms of Severe fever with thrombocytopenia syndrome (SFTS) patients, we conducted transcriptomic analysis of peripheral immunity in 14 SFTS patients, ranging from modal infection to severe and fatal disease. Our results observed the potential mechanism for the heterogeneity of clinical symptoms, which can further elucidate the interaction between viruses and hosts and contribute to clinical treatment.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

20 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

Platforms:

GPL30173 GPL18573

74 Samples

Download data: BW, TSV

(Submitter supplied) N6-Methyladenosine (m6A) is the predominant internal RNA modification in eukaryotic messenger RNAs (mRNAs) and plays a crucial role in mRNA stability. In this study, we reveal that m6A sites in the coding sequence (CDS) trigger CDS–m6A decay (CMD), a novel mRNA decay pathway that is distinct from previously reported m6A-dependent degradation mechanisms. Importantly, CDS m6A sites act considerably faster and more efficiently than those in the 3' untranslated region, which to date have been considered the main effectors of m6A-mediated RNA decay. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL18573

32 Samples

Download data: TSV

(Submitter supplied) Pituitary neuroendocrine tumors (PitNET) are among the most common intracranial tumors. Despite a frequently benign course, aggressive behavior occurs for unexplained reasons, especially in functional PitNET. Tumor behavior is known to be under the influence of the tumor microenvironment (TME). However, the relationship between TME cells and aggressive tumor behavior has not been adequately explored in PitNET. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

10 Samples

Download data: MTX, TSV

(Submitter supplied) Eicosanoids participate in the pathologies of inflammation and carcinogenesis and limiting their production by inhibiting group IVA cytosolic phospholipase A2 (cPLA2α) is a potential approach to cancer treatment. Here we report the synthesis of a new generation of thiazolyl ketone inhibitors of cPLA2α starting from compound GK470 (AVX235), and the discovery of a more potent and selective lead, GK420 (AVX420), with significant chemotherapeutic properties. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30173

24 Samples

Download data: TSV