GEO DataSets

(Submitter supplied) Background: Tissue biomarkers of immune checkpoint inhibitor (ICI) response are limited by tumor sample heterogeneity and availability. This study seeks to develop clinically actionable biomarkers in peripheral blood prior to ICI therapy initiation for recurrent/metastatic (R/M) head and neck squamous cell carcinoma (HNSCC), evaluating their association with treatment response and survival. Methods: This prospective multi-center study enrolled HNSCC patients before standard-of-care immunotherapy treatment. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platforms:

GPL21145 GPL33022

100 Samples

Download data: IDAT, TXT

(Submitter supplied) Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease.MicroRNAs play roles in the onset and progression of the disease. This study aimed to screen microRNA profiles and potential RNA networks for the diagnosis and treatment of NAFLD. Mice were high-fructose diet (HFrD) fed to induce NAFLD. MicroRNA expression profiles of the livers in HFrD mice and chow-diet fed mice were analyzed by RNA-seq. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: XLSX

(Submitter supplied) The most common genetic cause of both frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is a G4C2 repeat expansion in intron 1 of the C9orf72 gene. This repeat expansion undergoes bidirectional transcription to produce sense and antisense repeat RNA species. Both sense and antisense-derived repeat RNAs undergo repeat-associated non-AUG translation in all reading frames to generate five distinct dipeptide repeat proteins (DPRs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

14 Samples

Download data: CSV

(Submitter supplied) The goals of this study is to compare transcriptome profiles (RNA-seq) of seven 5-HT neuronal subpopulations in zebrafish whole brain. Tg(tph2:GFP) fish at 7 dpf were fixed in a recording chamber containing extracellular solution. The somata of 5-HT neurons from seven subpopulations (PT, SR-R, SR-M, SR-C, IR-R, IR-C, MO) were visualized under a fluorescence microscopy, then targeted and collected separately using glass electrode. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30614

71 Samples

Download data: XLS

(Submitter supplied) Bulk RNA-seq (PME-seq) generated for analysis in parallel with Array-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

180 Samples

Download data: TXT

(Submitter supplied) Systemic lupus erythematosus is a remitting relapsing autoimmune disease characterized by autoantibody production and multi-organ involvement. T cell epigenetic dysregulation plays an important role in the pathogenesis of lupus. We have previously demonstrated upregulation of the key epigenetic regulator EZH2 in CD4+ T cells isolated from lupus patients. To further investigate the role of EZH2 in the pathogenesis of lupus, we generated a tamoxifen-inducible CD4+ T cell Ezh2 conditional knockout mouse on the MRL/lpr lupus-prone background. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

3 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Acetaminophen (APAP) overdose is the major cause of drug-induced liver injury (DILI) and acute liver failure (ALF), and patients with advanced APAP toxicity rarely benefit from N-acetylcysteine (NAC), which is the first-line agent used in the clinic. Mesenchymal stromal cells (MSCs) and their extracellular vesicles (MSC-EVs) have shown promising effects in the treatment of DILI by decreasing neutrophil infiltration. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT

(Submitter supplied) Although mutations in human patatin-like phospholipase PNPLA6 are associated with hereditary retinal degenerative diseases, its mechanistic action in the retina is poorly understood. Here, we uncover the molecular mechanism by which PNPLA6 dysfunction disturbs retinal homeostasis and visual function. PNPLA6, by acting as a phospholipase B, regulates choline mobilization from phosphatidylcholine and subsequent choline turnover for phosphatidylcholine regeneration in retinal pigment epithelial (RPE) cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

2 Samples

Download data: TXT

(Submitter supplied) Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here, we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem cell (iPSC)-induced excitatory neurons. more...

Organism:

Pan troglodytes; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL30573

8 Samples

Download data: NARROWPEAK

(Submitter supplied) The gene expression profling between Control and 4,4'-Methylenebis(2-chlorobenzenamine) exposure for 4 weeks in liver of F1-TKm30 female mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

8 Samples

Download data: TXT

(Submitter supplied) The gene expression profiling between Control and 4,4'-Methylenebis(2-chlorobenzenamine) exposure for 4 weeks in liver of F1-TKm30 female mice transplanted with commercially available human hepatocytes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

9 Samples

Download data: TXT

(Submitter supplied) High histone acetylation is associated with high transcriptional activity. The lysine acetyltransferase KAT6B is known to be required for histone acetylation and KAT6B is essential for normal brain development. In this study we examined the effects of loss and gain of KAT6B on gene expression in forebrain neural stem and progenitor cells (NSPCs). We isolated NSPCs from the dorsal telencephalon of embryonic day 12.5 embryos, which is the primordium of the cerebral cortex, from mouse embryos that lacked KAT6B or overexpressed KAT6B. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

15 Samples

Download data: TXT

(Submitter supplied) The vagus nerves are important carriers of sensory information from the viscera to the central nervous system. Emerging evidence suggests that sensory signaling through the right, but not the left, vagus nerve evokes striatal dopamine release and reinforces appetitive behaviors. However, the extent to which differential gene expression within vagal sensory neurons contributes to this asymmetric reward-related signaling remains unknown. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32190

8 Samples

Download data: CSV, XLSX

(Submitter supplied) Neuroimmune interactions are critical regulators of tissue homeostasis and allergic inflammation, and group 2 innate lymphoid cells (ILC2s) have emerged as an important cell type for mediating these interactions. Here, we identified that the abundance of dopamine (DA) was negatively correlated with the number of circulating ILC2s and lung function in human. Dopamine potently suppressed lung ILC2 responses in mice, which was dependent on the expression of dopamine receptor DRD1. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

8 Samples

Download data: TAR, TSV

(Submitter supplied) This project focuses on the neurotoxic effects of methamphetamine (METH) abuse and its impact on the central nervous system. Methamphetamine is a highly addictive synthetic drug that can cause severe cognitive and behavioral changes, as well as neurodegenerative diseases. We conducted transcriptome sequencing on METH-treated primary neurons from tree shrews to investigate the underlying mechanisms of METH-induced neuronal damage.

Organism:

Tupaia belangeri

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24233

8 Samples

Download data: TXT

(Submitter supplied) Primary aldosteronism (PA) is the most prevalent cause of secondary hypertension. Its two main clinical forms are unilateral adenoma (UPA) and bilateral hyperplasia (BAH), which require markedly different medical treatments, so differentiating between the two is of utmost clinical importance. The current gold standard method for this is adrenal vein sampling (AVS), the application of which is hindered by limited availability and high skill requirements. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

36 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; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL32159 GPL19057

34 Samples

Download data: BW

(Submitter supplied) Exhausted CD8 T cells result from chronic antigen stimulation and have reduced ability to clear disease. The epigenetic regulation of the dysfunctional phenotype of exhausted CD8 T cells is a promising avenue for therapies aimed at reversing or preventing CD8 T cell exhaustion. Here, utilizing an in vitro model, we show global increase of the repressive histone modification H3K27me3 in CD8 T cell exhaustion as well as increased gene expression of the subunits of PRC2, the complex responsible for H3K27me3 deposition. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

14 Samples

Download data: BW

(Submitter supplied) Exhausted CD8 T cells result from chronic antigen stimulation and have reduced ability to clear disease. The epigenetic regulation of the dysfunctional phenotype of exhausted CD8 T cells is a promising avenue for therapies aimed at reversing or preventing CD8 T cell exhaustion. Here, utilizing an in vitro model, we show global increase of the repressive histone modification H3K27me3 in CD8 T cell exhaustion as well as increased gene expression of the subunits of PRC2, the complex responsible for H3K27me3 deposition. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32159 GPL19057

20 Samples

Download data: TXT

(Submitter supplied) Analysis of single cell RNA-seq, CITE-seq data and bulk RNA-seq data on cells isolated from the livers of mice following PBS and APAP (paracetamol/acetaminophen) administration. Spatial Transcriptomics analysis was performed using 10x Visium platform on mouse livers 48hrs post PBS or APAP administration. We also analysed single cell RNA-seq data on CD64+F4/80+ macrophages isolated from the livers of Trem2 fl/fl mice and CD64CRE Trem2 fl/fl mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24247 GPL21103

42 Samples

Download data: CSV, H5