GEO DataSets

(Submitter supplied) We performed ATAC-seq in a set of 25 gastric cancer cell lines to detect differential activation of regulatory programs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

25 Samples

Download data: BED, BIGWIG

(Submitter supplied) Sclerotinia sclerotiorum, the causal agent of white mould, is a necrotrophic fungal pathogen responsible for extensive crop loss. Current control options rely heavily on the application of chemical fungicides that are becoming less effective and may lead to the development of fungal resistance. In the current study, we used a foliar spray application of boron to protect Brassica napus (canola) from S. more...

Organism:

Brassica napus; Sclerotinia sclerotiorum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34395 GPL29911

18 Samples

Download data: TXT

(Submitter supplied) Thymic epithelial cells (TECs) are a critical functional component of the thymus’s ability to generate T cells for the adaptive immune system in vertebrates. However, no in vitro system for studying TEC function exists. Overexpressing the transcription factor FOXN1 initiates transdifferentiation of fibroblasts into TEC-like cells (iTECs) that support T cell differentiation in culture or after transplant. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30172

9 Samples

Download data: MTX, TSV

(Submitter supplied) Thymic epithelial cells (TECs) are a critical functional component of the thymus’s ability to generate T cells for the adaptive immune system in vertebrates. However, no in vitro system for studying TEC function exists. Overexpressing the transcription factor FOXN1 initiates transdifferentiation of fibroblasts into TEC-like cells (iTECs) that support T cell differentiation in culture or after transplant. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

13 Samples

Download data: CSV

(Submitter supplied) Osteoarthritis (OA) is a widespread age-related joint disease caused by the gradual loss of chondrocyte function along with age. Here, we found that UFMylation modification was lower-leveled in senescent cartilage, mediated chondrocyte senescence and OA phenotypes through targeting CAVIN1, which acted as a stimulator in chondrocyte senescence, mainly through promoting CPT1 expression and activating fatty acid β-oxidation (FAO). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) The gut microbiota is closely associated with digestion, metabolism, immunity, and host health. The imbalance of the microbial community in livestock directly affects their well-being and, consequently, productivity. The composition and diversity of the gut microbiota are influenced not only by host genetics but also by environmental factors such as the microbial complexity of the rearing environment, feeds, and antibiotics. more...

Organism:

Sus scrofa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20809

8 Samples

Download data: ZIP

(Submitter supplied) The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

41 Samples

Download data: CSV

(Submitter supplied) The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

66 Samples

Download data: TXT

(Submitter supplied) The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme in the spinal cord. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) To elucidate the mechanism by which EZH2 regulates the radiosensitivity of KDM6A-deficient ESCC cells, we established KYSE180-shEZH2 and control KYSE180-shluc cells. 48 hours after exposure to 6Gy IR, we performed gene expression profiling analysis using RNA-seq data from KYSE180-shEZH2 and control KYSE180-shluc.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) The dynamics of immune reprogramming in the breast cancer lung metastastic niche remains incomplete. We used MULTI-seq (McGinnis, Patterson, et al., Nature Methods, 2019) to perform multiplexed single-cell RNA-sequencing analysis of cryopreserved lung immune cells isolated from PyMT mice, freshly-isolated lung immune cells isolated from PyMT mice, and cryopreserved lung immune cells isolated from 4T1 tumor-bearing mice from the onset of primary tumorigenesis through the formation of macrometastatic lesions. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

38 Samples

Download data: CSV, MTX, TSV, TXT

(Submitter supplied) Understanding epithelial lineages in breast cancer and genotype-phenotype interactions requires direct measurements of the genome and transcriptome of the same single cells at scale. To achieve this, we developed wellDR-seq, the first high-genomic resolution, high-throughput method to simultaneously profile the whole genome and transcriptome of thousands of single cells. We profiled 17,427 single cells in 6 ER-positive breast cancer patients, which identified ancestral subclones in three patients that were from the luminal hormone responsive lineage, indicating a cell-of-origin. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

18 Samples

Download data: RDS

(Submitter supplied) Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. HCC incidence is on the rise, while treatment options remain limited. Thus, a better understanding of the molecular pathways involved in HCC development has become a priority to guide future therapies. While previous studies implicated the AP-1 (Fos/Jun) transcription factor family members c-Fos and c-Jun in HCC formation, the contribution of Fos-related antigens 1 and 2 (Fra-1/2) is unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

19 Samples

Download data: TSV

(Submitter supplied) Inflammatory responses, apoptosis, and oxidative stress, are key factors that contribute to hepatic ischemia/reperfusion (I/R) injury, which may lead to the failure of liver surgeries, such as hepatectomy and liver transplantation. The N6-methyladenosine (m6A) modification has been implicated in multiple biological processes, and its specific role and mechanism in hepatic I/R injury require further investigation. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

8 Samples

Download data: TXT

(Submitter supplied) Scaffold protein IQGAP3 mediates assembly of multiprotein complexes, orchestrating intracellular signaling pathways. Earlier we have found it to be overexpressed in lesional psoriatic skin. IQGAP3 is involved in cell proliferation and chemokine signaling that are key processes in psoriasis, so we decided to investigate the molecular basis of its role in psoriatic phenotype of keratinocytes. Transcriptome profiling of HaCaT keratinocytes allowed us to identify a wide range of psoriasis-associated pathways to be altered in IQGAP3-knockdown cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

5 Samples

Download data: CSV

(Submitter supplied) Precise genome editing is crucial for establishing isogenic human disease models and ex vivo stem cell therapy from the patient-derived human pluripotent stem cells (hPSCs). Unlike Cas9-mediated knock-in, cytosine base editor (CBE) and prime editor (PE) achieve the desirable gene correction without inducing DNA double strand breaks. However, hPSCs possess highly active DNA repair pathways and are particularly susceptible to p53-dependent cell death. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

5 Samples

Download data: CSV

(Submitter supplied) RNA-seq analysis compares gene expression of the snf22∆ and snf22-(D996A-E997A) mutants to the wild-type fission yeast (Schizosaccharomyces pombe).

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28961

9 Samples

Download data: XLSX

(Submitter supplied) We report the grobal gene expression in follicular (FO) B cells stimulated with CpG, IFNa, and CpG plus IFNa for 12 hours prior to the onset of PC differentiation. We found that stimulation with CpG plus IFNa upregulates metabolic processes compared to stimulation with CpG alone. This study highlight the pivotal role of IFNa in determining the fate of PC differentiation of TLR9-activated FO B cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

12 Samples

Download data: TSV, TXT

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

22 Samples

Download data: BIGWIG, TXT