GEO DataSets

(Submitter supplied) Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive but genetically simple pediatric central nervous system tumor, defined by biallelic inactivation of the chromatin regulator SMARCB1 with remarkably few other cooperating mutations. Despite its genetic homogeneity, ATRT exhibits profound clinical and epigenetic heterogeneity, with three major subgroups (ATRT-TYR, ATRT-MYC, and ATRT-SHH) defined by DNA methylation and transcriptional signatures. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

26 Samples

Download data: BW

(Submitter supplied) Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive but genetically simple pediatric central nervous system tumor, defined by biallelic inactivation of the chromatin regulator SMARCB1 with remarkably few other cooperating mutations. Despite its genetic homogeneity, ATRT exhibits profound clinical and epigenetic heterogeneity, with three major subgroups (ATRT-TYR, ATRT-MYC, and ATRT-SHH) defined by DNA methylation and transcriptional signatures. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: BW

(Submitter supplied) The formation of tertiary lymphoid structures (TLSs) in tumors is significantly correlated with prolonged patient survival, better prognosis, and improved response to immunotherapy. To assess the tumor microenvironment associated with TLS formation, we performed bulk RNA sequencing using archived FFPE human breast cancer tissues.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

16 Samples

Download data: TXT

(Submitter supplied) Compare control vs knockdown cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: XLSX

(Submitter supplied) To characterize transcriptional and chromatin accessibility changes that promote survival of residual cancer following chemotherapy, we performed single-cell multiomic profiling (snRNA+snATAC) on a cohort of non-malignant fallopian tube, treatment-naive, and neoadjuvant chemotherapy (NACT)-treated high-grade serous ovarian cancer (HGSOC) samples. From this analysis, we identified an epigenetic signature that precedes expression and defines the drug-tolerant persister state.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

30 Samples

Download data: H5, RDS, TSV

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

Organism:

Homo sapiens; Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

95 Samples

Download data: BED, BW

(Submitter supplied) FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Tregs). While mice exclusively express FOXP3 in Tregs, humans also transiently express FOXP3 in stimulated conventional CD4+ T cells (Tconvs). Mechanisms governing these distinct expression patterns remain unknown. Here, we performed CRISPR screens tiling the FOXP3 locus and targeting TFs in human Tregs and Tconvs to discover cis-regulatory elements (CREs) and trans-regulators of FOXP3. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

8 Samples

Download data: XLSX

(Submitter supplied) FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Tregs). While mice exclusively express FOXP3 in Tregs, humans also transiently express FOXP3 in stimulated conventional CD4+ T cells (Tconvs). Mechanisms governing these distinct expression patterns remain unknown. Here, we performed CRISPR screens tiling the FOXP3 locus and targeting TFs in human Tregs and Tconvs to discover cis-regulatory elements (CREs) and trans-regulators of FOXP3. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

10 Samples

Download data: XLSX

(Submitter supplied) Long-term control of viral replication relies on the efficient differentiation of memory T cells into effector T cells during secondary immune responses. Recent findings have identified T cell precursors for both memory and exhausted T cells, suggesting the existence of progenitor-like effector T cells. These cells can persist without antigenic challenge but expand and acquire effector functions upon recall immune responses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

52 Samples

Download data: CSV

(Submitter supplied) Chronic rhinosinusitis (CRS) is a common inflammatory disease of the nasal cavity and sinuses that affects millions of individuals worldwide. The complex pathophysiology of CRS remains poorly understood, with emerging evidence implicating diverse immune and epithelial cell types in the disease process. We employed single-cell RNA sequencing (scRNA-seq) in dissociated tissues to investigate the cellular and molecular heterogeneity of CRS with and without nasal polyps.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: TAR

(Submitter supplied) Current treatments for inflammatory bowel disease (IBD) primarily rely on systemic immunosuppression, which often exhibits limited efficacy and off-target toxicity. Here we present a bioengineered extracellular vesicle (EV) platform designed for inflammatory bowel-targeted delivery of dual-action therapeutics, enabling precise modulation of T cell responses to enhance IBD treatment efficacy. EVs derived from Wharton’s jelly mesenchymal stem cells ( WJ-MSCs) were engineered to display membrane-bound PD-L1 and encapsulate miRNA 27a-3p (miR-27a-3p). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: MTX, TSV

(Submitter supplied) Two decades of genetic studies in autism spectrum disorder (ASD) have identified over a hundred genes harboring rare risk mutations. Despite this substantial heterogeneity, transcriptomic and epigenetic analyses have identified convergent patterns of dysregulation across ASD post-mortem brain. To identify shared and distinct mechanisms of ASD-linked mutations, we assembled the largest patient hiPS cell cohort to date, consisting of 70 hiPS cell lines after stringent quality control representing 8 ASD-associated mutations, idiopathic ASD, and 20 lines from non-affected controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

464 Samples

Download data: CSV

(Submitter supplied) The dopaminergic system has key roles in human physiology and is implicated in a broad range of neurological and neuropsychiatric conditions that are increasingly investigated using induced pluripotent stem cell-derived midbrain models. To determine the similarity of such models to human systems, we undertook single cell and spatial profiling of first and second trimester fetal midbrain and compared it to in vitro midbrain models. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676

29 Samples

Download data: CSV, JPG, 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; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

12 Samples

Download data: BW, TXT

(Submitter supplied) Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer that associates with poor prognosis and a high risk of relapse with limited treatment options. While the induction of senescence, a state of arrested cell growth, is generally achieved by available anticancer treatments, senescence can adversely promote tumorigenesis through an upheld augmented inflammatory state called senescence-associated secretory phenotype (SASP). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: BW, TXT

(Submitter supplied) The genetic basis for many common autoimmune disorders has been uncovered by genome-wide association studies (GWAS), but GWAS do not reveal causal variants, effector genes, or the cell types impacted by disease-associated variation. We have generated 3D genomic datasets consisting of promoter-focused Capture-C, Hi-C, ATAC-seq, and RNA-seq and integrated these data with GWAS of 16 autoimmune traits to physically map disease-associated variants to the genes they likely regulate in over 50 human cell types. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

14 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) VHL has been known as a tumour suppressor gene, also is an essential gene for some proteolysis-targeting chimera (PROTAC) degraders. Here by using CRISPR-cas9 genome wide screening we find that VHL mutation results in strong proliferation defect by HIF1A . VHL MUT shows malfunction of mitochondria which can be restored by HIF1A inhibition. VHL MUT bear specific genetic vulnerabilities which are druggable and mainly HIF1A dependent. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

24 Samples

Download data: TXT

(Submitter supplied) This study investigates the resistance mechanisms to pan-KRAS inhibitors in colorectal cancer (CRC). We established a panel of patient-derived organoids (PDOs) and cell lines with differential sensitivity to pan-KRAS inhibitors. Integrated epigenomic (ChIP-seq for H3K27ac and H3K4me3) and transcriptomic (RNA-seq) profiling revealed that enhancer remodeling drives compensatory activation of the mevalonate (MVA) pathway in resistant models. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

12 Samples

Download data: BW, XLSX

(Submitter supplied) Tumors are continuously evolving through their course of progression and treatment, a major process contributing to resistance to therapy. Recent studies brought into focus the importance of non-genetic adaptive mechanisms, by which tumors acquire resistance via rewiring transcriptional programs. To dissect these adaptive processes in the individual breast cancer patients, we combined longitudinal transcriptomics with temporal pattern analysis.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

84 Samples

Download data: XLSX

(Submitter supplied) HGC-27 GC cells were stimulated with Helicobacter pylori-lipopolysaccharide (Hp-LPS). PANDORA-seq sequencing was employed to elucidate the potential roles of these relatively uncharacterized novel small non-coding RNAs (sncRNAs) in Hp-infected gastric cancers. RNA-seq was performed to identify diffferentially-expressed gene in Hp-infected gastric cancers.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

12 Samples

Download data: TXT