GEO DataSets

(Submitter supplied) Lung cancer is the most currently diagnosed cancer type among adults and the most common cause of death from cancer worldwide. Poor lung cancer patients’ outcomes and survival rates demand discovery of new biomarkers for the specific, significant, and non-invasive detection of non-small cell lung cancer (NSCLC) progression. Determination of cell lines' relationship to genomic changes in tumors could be valuable for functional and therapeutic discoveries. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21697

15 Samples

Download data: TXT

(Submitter supplied) Background: Hepatocellular adenomas (HAs) are tumors that can develop under different conditions, including in patients harboring a germline mutation in HNF1A. However, little is known about the pathogenesis of such disease. This work aims at better defining what mechanisms lie under the development of this condition. Results: 6 HAs were sampled from the liver of a 17-year-old male affected by diabetes and multiple hepatic adenomatosis harboring the heterozygous pathogenic germline variant c.815G>A, p.(Arg272His) in HNF1A which has a dominant negative effect. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

7 Samples

Download data: CSV

(Submitter supplied) In this study, we employed RNA-seq to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: TSV

(Submitter supplied) In this study, we employed ChIP-seq for histone modifications related to gene activation, such as H3K4me1, H3K4me3, and H3K27Ac, to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) In this study, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) to investigate the role of N6-methyladenine (6mA) in chromatin accessibility under hypoxic conditions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: BED, BIGWIG, CSV

(Submitter supplied) This dataset encompasses comprehensive analyses of the epigenetic mark N6-methyladenine (6mA) in human cell lines, focusing on its role under hypoxic conditions and its association with cancer progression. Addressing the challenge of 6mA's low abundance in mammals, we have innovated the 6mA-ChIP-exo-5.1 method. This technique enhances the sensitivity and accuracy of 6mA detection, employing exonuclease-dependent antibody-based approaches combined with whole genome amplification (WGA) to minimize potential noise and false positives.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

10 Samples

Download data: BED, BIGWIG

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

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21697 GPL17303 GPL18573

15 Samples

Download data: BROADPEAK, BW

(Submitter supplied) Sp140 is a lymphocytic-restricted protein, an epigenetic reader working as a corepressor of genes implicated in inflammation and orchestrating macrophage transcriptional programs to maintain cellular identity. Reduced Sp140 expression is associated both to autoimmune diseases and blood cancer. However, the molecular mechanisms that link Sp140 altered protein levels to detrimental effects on the immune response and cellular growth, as well as the interactors through which Sp140 promotes gene silencing, remain elusive. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

4 Samples

Download data: BW

(Submitter supplied) Objective. To investigate the epigenetic footprint of idiopathic inflammatory myopathies (IIM) through characterization of circulating extracellular vesicles (EVs) and the expression of EV-derived small non-coding RNAs (sncRNAs).

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21697

92 Samples

Download data: XLSX

(Submitter supplied) Local and systemic immunosuppression are prominent features of pancreatic cancer, rendering anti-tumor effector cells inactive and immunotherapeutic approaches ineffective. The spleen, an understudied point of antigen-presentation and T cell priming in humans, holds particular importance in pancreatic cancer due to its proximity to the developing tumor. As main effectors of antigen presentation, dendritic cells display antigens to lymphocytes, thereby bridging the innate and adaptive immune response. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

7 Samples

Download data: MTX, TSV

(Submitter supplied) A total of four human melanoma liver metastasis (MLiM) formalin-fixed paraffin-embedded (FFPE) sections were analyzed using Nanostring GeoMx digital spatial profiling (NGDSP). The FFPE tissues were obtained from patients who underwent surgery and were pathological diagnosed with MLiM. Patients who had received any preoperative therapy were excluded. In each region of interest (ROI), two areas of interest (AOI)s were defined by HepPar1+ (hepatocytes); HMB45+ (melanoma cells) staining. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

43 Samples

Download data: XLSX

(Submitter supplied) Purpose: Breast cancers with ESR1 mutations are resistant to antiestrogen therapy. We aimed to investigate the association of ESR1 mutations with resistance to CDK4/6 inhibitors (CDK4/6i) using real-world data analysis and experimental validation. Patients and Methods: A total of 3,958 patients with estrogen receptor-positive (ER+) metastatic breast cancer with DNA sequencing data were analyzed. Breast tumor DNA and circulating tumor (ct) DNA were sequenced using the Tempus xT tumor assay and Tempus xF liquid biopsy, respectively. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

36 Samples

Download data: TSV

(Submitter supplied) The goal of this study is to compare the different biological functions between nuclear (ICD)-TYRO3- and kinase dead (KD)-TYRO3-overexpressed cells by BRD3 occupancy profiling. We revel that ICD-TYRO3-overexpressed cell were particularly enriched in negatively regulate cell death, regulation of cell cycle, regulation of vascular permeability, positively regulation of EMT, cell-cell adhesion, and regulation of phosphorylation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

2 Samples

Download data: TXT

(Submitter supplied) Somatic mutations in ARID1A (AT-rich interactive domain-containing protein 1A) are present in approximately 25% of bladder cancers (BC) and are associated with poor prognosis. With a view to discover effective treatment options for ARID1A-deficient BC patients, we set out to identify targetable effectors dysregulated consequent to ARID1A deficiency. Integrative analyses of ARID1A depletion in normal organoids and data mining in publicly available datasets revealed upregulation of DNA repair and cell cycle-associated genes consequent to loss of ARID1A and identified CHEK1 (Checkpoint kinase 1) and chromosomal passenger complex member BIRC5 (Baculoviral IAP Repeat Containing 5) as therapeutically drug-able candidate molecular effectors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21697 GPL17303

40 Samples

Download data: TXT

(Submitter supplied) Glioblastoma (GBM) is the deadliest brain cancer, driven in part by GBM stem cells (GSCs) that contribute to therapeutic resistance and tumor recurrence. Effective targeting and elimination of GSCs hold promise for preventing GBM recurrence and achieving potential cures. In this study, we explored the role of the epigenetic regulator SUV39H1 in GSC maintenance and GBM progression. We observed that SUV39H1 is upregulated in GBM samples compared to normal brain tissues. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

4 Samples

Download data: BED, BW

(Submitter supplied) Memory T and B cells in lymphoid and mucosal tissues maintain long-term protection, though their generation following vaccination remains challenging to assess in humans. Here, we investigated immune memory generated to COVID-19 mRNA vaccines across blood, lymphoid organs, and lungs from 42 vaccinated organ donors aged 23-86, of whom 57% were previously infected with SARS-CoV-2. Using high-dimensional profiling, we reveal that Spike (S)-reactive memory T cells distribute in lymphoid organs and lungs, variably express tissue resident markers based on infection history, and exhibit site-specific compositions of effector and regulatory memory T cells. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL21697 GPL24676

82 Samples

Download data: TXT

(Submitter supplied) Pediatric sarcomas present heterogeneous morphology, genetics and clinical behavior posing a challenge for an accurate diagnosis. DNA methylation is an epigenetic modification that coordinates chromatin structure and regulates gene expression, determining cell type and function. DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) was applied to 122 pediatric sarcomas referred to a reference pediatric oncology hospital. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34281 GPL21697

14 Samples

Download data: CSV

(Submitter supplied) We were interested in transcriptional changes after depletion of histone acetyltransferase KAT2A in human colorectal cancer. Therefore, we utilized HCT116 cells as model, and analyzed global alterations of gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

6 Samples

Download data: XLSX

(Submitter supplied) We aimed to create an ovary cell atlas using publicly available RNA-seq data. To complement the data we sequenced 2 ovary tissue samples from patients undergoing elective surgery at the JR hospital in Oxford. We applied single-nucei sequencing using the 10x Chromium technology.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

2 Samples

Download data: H5

(Submitter supplied) RNA modifications regulate how RNAs metabolize and function to impact development and diseases. N6,2’-O-dimethyladenosine (m6Am) is one such modification and despite being abundant, m6Am function remains unclear. Here, we identified cleavage and polyadenylation factor, PCF11 as a m6Am-specific binding protein. Direct quantification of mature versus nascent RNAs revealed that m6Am does not regulate mRNA stability but promotes transcription of nascent RNAs. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL20795 GPL21697

36 Samples

Download data: BEDGRAPH, XLSX