GEO DataSets

(Submitter supplied) Background. Circular RNAs (circRNAs) play an important role in the occurrence and development of diseases. However, the role of circRNAs in male smokers with chronic obstructive pulmonary disease (COPD) remains unclear. Methods. Stable COPD patients and healthy controls were recruited. Peripheral blood mononuclear cells (PBMCs) were extracted. After high-throughput RNA sequencing (RNA-Seq) of PBMCs, a bioinformatics method was used to analyse differentially expressed (DE) circRNAs (DEcircRNAs) and mRNAs (DEmRNAs). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

10 Samples

Download data: FA, FASTA, GTF, TXT

(Submitter supplied) The study is designed to understand the role of TET mediated demethylation and its intricate interplay with histone enhancers and loci-specific 5-hmC levels of candidate genes in breast cancer.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: NARROWPEAK

(Submitter supplied) Analysis of MKN-45 cells following SIX2 stable overexpression or not. SIX2 regulates various mRNA expression in MKN-45 cells.Results provide insight into the role of SIX2-involved mechanisms underlying SIX2-mediated effects on gastric cancer stemness.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLS

(Submitter supplied) We report genome-wide distribution of newly discovered O-GlcNAcylated H4 at threonine 71 (H4T71Gc) in mouse embryonic stem cells (mESCs, J1 line) cultured in 25 mM glucose (mESCs-25mMG) or 1 mM glucose (mESCs-1mMG) condition, human embryonic stem cells (hESCs, H9) and human induced-pluripotent stem cells (hiPSCs, 201B7). We found that H4T71Gc preferentially localize to gene regions, especially those with relatively high expression levels. more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL20301 GPL21103

8 Samples

Download data: BED, BIGWIG

(Submitter supplied) Localization of Fusobacterium nucleatum in the placenta may be associated with pregnancy complications including preeclampsia (PE), but its specific pathobiology is unknown. Our aim was to analyze the effect of Fusobacterium nucleatum on HUVEC cells to further elucidate placental dysfunction in the context of Fusobacterium nucleatum infestation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Pluripotent stem cell (PSC)-derived electrically excitable cells provide a unique window into human disease and development, but they remain electrically immature compared to their in vivo counterparts, partially due to the lack of chronic stimulation. New classes of on-demand, electrically active biomaterials are being employed to enhance cell functions, and here, we fabricated biocompatible, electrospun polymer nanofibers containing light-reactive reduced graphene oxide (rGO). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

23 Samples

Download data: CSV

(Submitter supplied) This study aimed to find diagnostic biomarkers for predicting cardiac surgery-associated acute kidney injury in children. We found that the change of exomiRs level in circulatory system occurred in the early stage after cardiac operation, and the changes of hsa-miR-184 and hsa-miR-6766-3p content in circulatory system could predict CSA-AKI well.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

(Submitter supplied) Chronic myeloid leukemia (CML), caused by BCR::ABL1 fusion gene, is known to regulate disease progression by altering the expression of genes. However, the molecular mechanisms underlying these changes are largely unknown. In this study, we identified RNA Exonuclease 5 (REXO5) as a novel gene with elevated mRNA expression levels in chronic myeloid leukemia (CML) patients. Additionally, using the REXO5 knockout (KO) K562 cell lines, we revealed a novel role for REXO5 in the DNA damage response (DDR). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: IDAT, XLSX

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30173 GPL30172

17 Samples

Download data: MTX, TSV

(Submitter supplied) While immunotherapy has shown efficacy in non-small cell lung cancer (NSCLC) patients, many respond only partially or not at all. One limitation in improving outcomes is the lack of a complete understanding of factors regulating immune checkpoint targets. Here, we sought to address a possible link between an environmental chemical receptor implicated in NSCLC and immune regulation, the aryl hydrocarbon receptor (AhR), and a known but counterintuitive mediator of immunosuppression, IFN , in regulation of two immune checkpoints, PD-L1 and the IDO1, in lung adenocarcinoma (LUAD). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: XLSX

(Submitter supplied) Intercellular communication drives directed flows of information that are mediated by intracellular gene modules, in turn triggering outflows of other signals. Methodologies to describe such intercellular flows are severely lacking. We present FlowSig, a method that infers communication-driven intercellular flows from scRNA-seq using graphical causal modeling and conditional independence. We used human cortical organoid samples collected at D18 and D35 to demonstrate the functions of FlowSig.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: CSV, H5AD, MTX, TXT

(Submitter supplied) Genes encoding subunits of SWI/SNF chromatin remodeling complexes are mutated in nearly 25% of cancers. The SWI/SNF subunit SMARCB1 is the driving mutation in nearly all cases of rhabdoid tumor (RT), highly malignant cancers of childhood. While loss of SMARCB1 drives cancer, its absence also creates unique dependencies, which can illuminate mechanism and reveal potential therapeutic vulnerabilities. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Multi-Omics analysis to gain novel insights into clear cell renal carcinoma aetiology and progression. The DNA methylation data of 121 clear clear renal carcinoma (ccRCC) were integrated with WGS and transcriptomic data using Multi-Omics Factor Analysis (MOFA) to detect the inter-patient variations related to aetiological and disease progression related factors.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

121 Samples

Download data: IDAT, TSV

(Submitter supplied) Cisplatin-based chemotherapy is the first-line treatment for patients with advanced bladder cancer, but the development of cisplatin-resistance limits its anti-tumor effects. Previous studies have shown that cisplatin resistance in bladder cancer may be related to a variety of factors, such as changes in drug transport and metabolism, enhancement of DNA repair mechanisms, changes in cell cycle regulation, inhibition of apoptosis, and epigenetic modification. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

(Submitter supplied) Integration of multiple data modalities in a spatially informed manner remains an unmet need for exploiting spatial multi-omics data. Here, we introduce SpatialGlue, a novel graph neural network with dual-attention mechanism, to decipher spatial domains by intra-omics integration of spatial location and omics measurement followed by cross-omics integration. We demonstrate that SpatialGlue can more accurately resolve spatial domains at a higher resolution across different tissue types and technology platforms, to enable biological insights into cross-modality spatial correlations.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

8 Samples

Download data: CSV, H5AD, JPG, MTX, PNG, TSV

(Submitter supplied) Pulmonary hypertension (PH) is a common complication of systemic sclerosis (SSc) and a leading cause of mortality among patients with this disease. PH can also occur as an idiopathic condition (idiopathic pulmonary arterial hypertension, iPAH). We sought to investigate the transcriptomic alterations in PH vascular populations to understand cellular mechanisms underlying pathobiology of systemic sclerosis associated and idiopathic pulmonary hypertension.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20795 GPL24676 GPL18573

33 Samples

Download data: H5

(Submitter supplied) T cell senescence is a dysfunctional state distinct from exhaustion, yet the mechanism driving CD8+ T cell senescence directly in tumor microenvironment and its impact on cancer prognosis remain elusive. Here, by using single cell RNA sequencing of human cervical cancer tissues, we found that concurrent chemoradiotherapy (CCRT) specifically promoted CD8+ T cell senescence, which is driven by a subpopulation of ACKR2+ CCRT-resistance tumor cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(Submitter supplied) Background and aims: Oxidative stress triggers nonalcoholic steatohepatitis (NASH) and fibrosis. Previous animal studies demonstrated that the transcription factor NRF2, the master regulator of antioxidant response, protects against NASH and fibrosis. S217879, a new generation NRF2 activator has been recently shown to trigger NASH resolution and to reduce established fibrosis in rodents. Our aim was to evaluate the therapeutic potential of S217879 in human metabolic associated fatty liver disease (MAFLD) and its underlying mechanisms using the relevant experimental 3D model of patient-derived precision cut liver slices (PCLS). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: TXT

(Submitter supplied) Oral cavity squamous cell carcinoma (OSCC) is a complex and dynamic disease characterized by clinicopathological and molecular heterogeneity. Spatial and temporal heterogeneity of cell subpopulations has been associated with cancer progression and implicated in the prognosis and therapy response. Emerging evidence indicates that aberrant epigenetic profiles in OSCC may foster an immunosuppressive tumor microenvironment by modulating the expression of immune-related long non-coding RNAs (lncRNAs). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

92 Samples

Download data: IDAT, TXT

(Submitter supplied) We performed gene set enrichment and differential expression analysis to identify biological pathways associated with locoregional recurrence in primary breast tumors. A custom Affymetrix microarray genechip was used to assess the gene expression of each tumor sample.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15048

637 Samples

Download data: CEL