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Items: 1 to 20 of 1488

  • The following term was not found in GEO DataSets: Tunyasuvunakool.
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1.

Cancer-associated RUNX3 missense mutation promotes the expansion of isthmus stem cells and inhibits their differentiation in the stomach

(Submitter supplied) Background & Aims: RUNX transcription factors play pivotal roles in embryonic development and neoplasia. We previously identified the single missense mutation R122C in RUNX3 from human gastric cancer. However, how RUNX3R122C mutation disrupts stem cell homeostasis and promotes gastric carcinogenesis remained unclear. Methods: To understand the oncogenic nature of this mutation in vivo, we generated the RUNX3R122C knock-in mice. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28457
6 Samples
Download data: XLSX
Series
Accession:
GSE190081
ID:
200190081
2.

EndoTime: Non-categorical timing estimates for endometrial tissue during the secretory phase

(Submitter supplied) It is estimated that 1% of women suffer from Recurrent Pregnancy Loss (RPL), a debilitating condition currently defined as three or more consecutive miscarriages with no known preventative treatment. However, as 65% of women are able to successfully bear children following diagnosis the risk of RPL appears to be relatively transient. The foundation for embryo implantation is the endometrium – a complex heterogenous tissue that is also transitory in nature, and which dynamically cycles between phases of proliferation, maintenance and elimination. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
108 Samples
Download data: XLSX
Series
Accession:
GSE180485
ID:
200180485
3.

Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling

(Submitter supplied) Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. more...
Organism:
Danio rerio
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL23085 GPL30372
2 Samples
Download data: BEDGRAPH, TSV
Series
Accession:
GSE179673
ID:
200179673
4.

A novel whole blood gene expression signature for asthma, dermatitis and rhinitis multimorbidity in INMA cohort

(Submitter supplied) Allergic diseases correspond to a broad range of hypersensitivity reactions, often occurring as co-morbidities. Investigation of the molecular basis of allergy is a challenge because of its highly heterogeneous nature. We combined large-scale and high-throughput gene expression technology and systems biology approaches to retrieve relevant biomarkers and signalling pathways.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL17586
201 Samples
Download data: CEL
Series
Accession:
GSE141631
ID:
200141631
5.

A novel whole blood gene expression signature for asthma, dermatitis and rhinitis multimorbidity in BAMSE cohort

(Submitter supplied) Allergic diseases correspond to a broad range of hypersensitivity reactions, often occurring as co-morbidities. Investigation of the molecular basis of allergy is a challenge because of its highly heterogeneous nature. We combined large-scale and high-throughput gene expression technology and systems biology approaches to retrieve relevant biomarkers and signalling pathways.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL17586
256 Samples
Download data: CEL
Series
Accession:
GSE141623
ID:
200141623
6.

RNA-sequencing of cells derived from dermis and postmortem dura mater from the same subject

(Submitter supplied) Patient-derived cells hold great promise for precision medicine approaches in human health. Fibroblast cells have been a major source of human cells for reprogramming and differentiating into specific cell types for disease modeling. Such cells can be isolated at various stages during life (presymptomatic, symptomatic, and advanced disease) and thus can potentially be used to model different phases of disease progression. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
8 Samples
Download data: SF
Series
Accession:
GSE178933
ID:
200178933
7.

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]

(Submitter supplied) Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platforms:
GPL24247 GPL21493
23 Samples
Download data: CGMAP
Series
Accession:
GSE154520
ID:
200154520
8.

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RNA-seq]

(Submitter supplied) Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
12 Samples
Download data: TAR
Series
Accession:
GSE154519
ID:
200154519
9.

Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [ATAC-seq]

(Submitter supplied) Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19057
12 Samples
Download data: BW
Series
Accession:
GSE154518
ID:
200154518
10.

Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [ST]

(Submitter supplied) To illuminate the evolutionary trajectory of LUAD from AIS to IAC, high-throughput scRNA-seq and ST data were generated and integrated to create a large-scale, single-cell spatiotemporal atlas of LUAD. We compiled a multi-omics atlas of the early-stage LUAD invasion process that reflects the heterogeneity of cancer cells, the competitive polyclonal origin of LUAD, signalling interactions between cancer cells and the TME, and the pseudo-chronological nature of LUAD invasion. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21290
6 Samples
Download data: CSV, MTX, TSV
Series
Accession:
GSE189487
ID:
200189487
11.

Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [scRNA-seq]

(Submitter supplied) To illuminate the evolutionary trajectory of LUAD from AIS to IAC, high-throughput scRNA-seq and ST data were generated and integrated to create a large-scale, single-cell spatiotemporal atlas of LUAD. We compiled a multi-omics atlas of the early-stage LUAD invasion process that reflects the heterogeneity of cancer cells, the competitive polyclonal origin of LUAD, signalling interactions between cancer cells and the TME, and the pseudo-chronological nature of LUAD invasion. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
9 Samples
Download data: MTX, TSV
Series
Accession:
GSE189357
ID:
200189357
12.

Transcriptomic and Single-Cell Analysis Reveals Regulatory Networks and Cellular Heterogeneity in Mouse Sjögren’s Syndrome Salivary Glands

(Submitter supplied) Our scRNA-seq and bulk RNA-seq studies have revealed key pathways, mediators, new biomarkers, and have uncovered the complex nature of the cellular populations in the SMG that are likely to drive the progression of SS.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
8 Samples
Download data: H5, TXT
Series
Accession:
GSE175649
ID:
200175649
13.

Deleting DNMT3A in CAR T cells prevents exhaustion and 1 enhances antitumor activity

(Submitter supplied) Whole-genome bisulfite sequencing data generated from WT and DNMT3A KO or IL-10 KO CAR T cells. These data were generate at early (week 1) and later (week 4) time points during in vitro serial stimulation of the CAR T cells, or after infusion into tumor bearing mice. These data document the DNA methylation changes that are coupled to the functional decline in CAR T cells during their sustained stimulation, and the causal nature of DNMT3A-specific methylation in mediating the functional impairment of the CAR T cells.
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24676
41 Samples
Download data: BED
Series
Accession:
GSE184568
ID:
200184568
14.

Trajectories of partial and full EMT of mammary tumor cells in the MMTV-PyMT mouse model

(Submitter supplied) Epithelial-mesenchymal transition (EMT) is a multistep process of cell de-differentiation which confers carcinoma cells with a variety of malignant characteristics. Due to the transient and reversible nature of the process, cancer cells may transit between various stages of an EMT continuum, including epithelial, partial EMT or full EMT, and the actual status of cancer cells, the kinetics of cellular state transition in vivo and the consequences thereof have remained elusive. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
504 Samples
Download data: TXT
Series
Accession:
GSE171940
ID:
200171940
15.

STAT5 regulation of tumor associated macrophage function in murine models of breast cancer

(Submitter supplied) In breast cancer, interactions between tumor cells and surrounding stromal cells, such as macrophages, are critical for tumor growth, progression, and therapeutic response. Recent studies have highlighted the complex nature and heterogeneous populations of macrophages associated with both tumor promoting and tumor inhibiting phenotypes. Identifying the specific signaling pathways that regulate macrophage function within the tumor microenvironment will lead to new approaches that suppress tumor promoting functions while enhancing their anti-tumor functions. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24247
15 Samples
Download data: TXT
Series
Accession:
GSE171428
ID:
200171428
16.

Resolving the Difference Between Left-sided and Right-sided Colorectal Cancer by Single-cell Sequencing

(Submitter supplied) Colorectal cancers (CRCs) exhibit differences in incidence, pathogenesis, molecular pathways and outcome depending on the location of the tumor. The transcriptomes of 27,927 single human CRC cells, from three left-sided and three right-sided CRC patients were profiled by scRNA-seq. Right-sided CRC harbors a significant proportion of exhausted CD8 T cells of a highly migratory nature. One cluster of cells from left-sided CRC exhibiting states preceding exhaustion and a high ratio of “pre-exhausted” to exhausted T cells were favorable prognostic markers. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24676
6 Samples
Download data: MTX, TSV
Series
Accession:
GSE188711
ID:
200188711
17.

Antisense RNAs influence promoter usage of their counterpart sense genes in cancer

(Submitter supplied) Natural antisense transcripts (NATs) are those RNAs transcribed from the same locus, but in the opposite direction to a sense gene transcript. non-coding NATs (ncNATs) have been reported to modulate key biological events such as cell differentiation and carcinogenesis through gene expression regulation; nevertheless, their actual impact on cancer remains largely unknown. Due to their low expression levels and their overlap with sense genes, the study of ncNATs using RNA-seq is challenging. more...
Organism:
Homo sapiens
Type:
Other
Platform:
GPL11154
12 Samples
Download data
Series
Accession:
GSE174338
ID:
200174338
18.

SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity [SMART-Seq]

(Submitter supplied) The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, our understanding of how the chromatin is organized to prohibit the reversal of the developmental program remains limited. Specifically, the totipotency to pluripotency transition marks one of the most dramatic events to the chromatin, yet the nature of histone changes and regulation underlying this process are only partly characterized. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19057
10 Samples
Download data: TXT
Series
Accession:
GSE187521
ID:
200187521
19.

Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia

(Submitter supplied) We examined the effects of antipsychotic medications on the cell-specific epigenomics and transcriptomics in the frontal cortex of schizophrenic subjects.
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL20301
700 Samples
Download data: BW, TXT
Series
Accession:
GSE174407
ID:
200174407
20.

Native MOWChIP-seq: Genome-wide profiles of key protein bindings reveal functional differences among various brain regions

(Submitter supplied) Here we developed a low-input ChIP-seq technology and associated protocol for profiling RNA Polymerase II, transcription factor, or enzyme binding at the genome scale. The new approach, termed native MOWChIP-seq or nMOWChIP-seq, produces genome-wide binding profiles using as few as 1000 cells.
Organism:
Homo sapiens; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20301 GPL21103 GPL24676
48 Samples
Download data: BW
Series
Accession:
GSE172224
ID:
200172224
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