GEO DataSets

(Submitter supplied) Through immunoprecipitation of epitope-tagged ADAR3 protein, several ADAR3-bound RNAs have been reported till date. However, exogenous expression of proteins are usually associated with altered gene expression profiles and thus, can influence binding profiles of RNA-binding proteins (RBPs) being studied. Here, we used affinity-purified antibody to pull down ADAR3 endogenously expressed in U373 glioblastoma cells and identified transcripts significantly enriched in the ADAR3 immunoprecipitants over control. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

12 Samples

Download data: CSV

(Submitter supplied) Diffuse intrinsic pontine glioma (DIPG) is one of the devastating childhood cancers. Radiation therapy remains the only effective treatment yet provides a 5-year survival rate of only1%. Several clinical trials have attempted to enhance radiation anti-tumor activity using radiosensitizing agents, though none have been successful in doing so. Given this, there is a critical need for identifying effective therapeutics to enhance radiation sensitivity for the treatment of DIPG. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL24676 GPL18573

17 Samples

Download data: BIGWIG, CSV

(Submitter supplied) To enlarge our understanding on the effect of TLR1/2 stimulation to human chondrocytes and how NOS inhibition blocks this stimulatory effects, we planned to apply RNAseq analysis to human chondrocytes that are treated with TLR1/2 agonists and NOS inhibitor.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) Activating Transcription Factor 4 (ATF4) is a transcription factor that regulates cellular responses to nutrient deficiency, endoplasmic reticulum stress and oxidative stress. At the organism level, it is implicated in processes such as hematopoiesis, skeletogenesis, eye development, memory, muscle atrophy, and carbohydrate and lipid metabolism. Here, we carried out a massively parallel reporter assay (MPRA) to identify allelic regulatory effects of human genetic variants that reside in ATF4 binding sites identified in ChIP-Seq experiments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

14 Samples

Download data: 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; Methylation profiling by high throughput sequencing

Platforms:

GPL20301 GPL24676 GPL18573

20 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Somatic mutations acquired by hematopoietic stem cells (HSCs) are commonly found over the course of a lifespan. Some of these clones will outgrow through a process known as clonal hematopoiesis (CH) and produce mutated immune cell progeny, which will shape host immunity. Individuals with CH are asymptomatic but have increased risk of developing leukemia, cardiovascular and pulmonary inflammatory diseases, and severe infections. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: XLS

(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

Platform:

GPL18573

53 Samples

Download data: TXT

(Submitter supplied) Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Bulk RNA-sequencing was performed on STAR+ and STAR- cells after 5 days and after 12 days.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

11 Samples

Download data: TXT

(Submitter supplied) Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Bulk RNA-sequencing was performed on STAR populations after 5 days and after 12 days of plating single STAR+ or STAR- cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

21 Samples

Download data: TXT

(Submitter supplied) Human engineered CRC organoids were equipped with the intestinal stem cell reporter STAR reflecting transcriptional activity of ASCL2. Bulk ATAC-sequencing was performed on STAR populations after 5 days and after 12 days of plating single STAR+ or STAR- cells.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

21 Samples

Download data: TXT

(Submitter supplied) We comparatively evaluated transcriptomes from renal biopsies obtained from patients with T2DN or HN, main causes of CKD, and control renal tissues (n=6 per group). RNA was extracted from formalin-fixed and paraffin-embedded kidney samples and processed for RNA sequencing. Principal component analysis effectively separated diseased and control tissues. Gene and protein expression profiles revealed that EMT-related markers were upregulated in both diseases. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

18 Samples

Download data: TXT

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

57 Samples

Download data

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) Solid tumors are composed of cancer cells and host immune cells that are distributed in a non-uniform pattern. Although this spatial heterogeneity may reflect mutational variations in cancer cells, mechanisms that direct the recruitment of immune cells to distinct regions within a tumor remain poorly understood. Here, we show that microbial-host interactions define tumor nests enriched in immune cells, and the distribution of microbes within tumors parallels the spatial heterogeneity of intratumoral lymphoid and myeloid cell populations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) In this study, we identified various cell clusters in human normal/sporadic TAA ascending aorta samples by single-cell RNA sequencing (scRNA-seq), and discovered the senescent vascular smooth muscle cells (VSMCs) significantly increased in TAA samples. Then we explored the molecular basis of TAA progression, and recognized the key regulators and pathways involved in the TAA progression regulation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: CSV

(Submitter supplied) In this study, we investigated the regulation of interleukin-18 (IL-18) expression, crucial for intestinal barrier integrity, in inflammatory bowel disease (IBD). Through experiments with Caco-2 cells, we demonstrated that HIF1α-mediated IL18 expression induced by F. prausnitzii was dependent on HIF1α, suggesting a potential role for butyrate-producing gut bacteria in promoting mucosal healing in IBD.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

32 Samples

Download data: TXT

(Submitter supplied) BACKGROUND: Cardiac reprogramming is a technique to directly convert non-myocytes into myocardial cells using genes and/or small molecules. This intervention provides functional benefit to the rodent heart when delivered at the time of myocardial infarction or activated transgenically up to 4 weeks after myocardial infarction. Yet, several hurdles have prevented the advancement of cardiac reprogramming for clinical use. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL18573

19 Samples

Download data: TXT

(Submitter supplied) AZA treatment in AML cell lines led to a delayed expression of ERE transcripts. Autophagy inhibition resulted in a greater abundance of ERE transcripts, triggered pro-inflammatory responses, and improved the cytotoxic activity of AZA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) Endothelial cells (ECs) are by definition plastic and multipotent. EC plasticity was evaluated by stimulating EC to physiological and pathological stress coupled with antiproliferative therapies.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: MTX, TSV, TXT