GEO DataSets

(Submitter supplied) We have completed the Human lncRNA microarray analysis of the 4 samples that you submitted. Total RNA from each sample was quantified using the Nanodrop 1000 and the RNA integrity was assessed by Agilent 2100 Bioanalyzer. About 5 μg total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with Nimblegen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the Nimblegen wash buffer kit. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL35135

4 Samples

Download data: CALLS, PAIR, XLS

(Submitter supplied) Cigarette smoke has been demonstrated to stimulate the growth of existing bladder tumors by enhancing the survival and proliferation of cancer cells through the action of carcinogens present in smoke. Concurrently, Fatty Acid Synthase (FASN), a key enzyme in fatty acid synthesis crucial for lipid metabolism, exhibits dysregulation in various cancer types, often correlating with aggressive phenotypes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) Colorectal cancer (CRC) incidence is rising globally and anticipated to become the leading cause of cancer death in younger individuals. Potential risk factors are diet induced obesity and altered microbiomes that lead to accumulation of toxic metabolite accumulation. However, how ammonia and other microbial metabolites impact key signaling pathways, such as TGF-β signaling, to promote CRC remains unclear. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: TXT

(Submitter supplied) Purpose: Localized diseases are affected by and affect the systemic environment via blood circulation. In our studies, we explored the differences in different types of circulating serum RNAs between wet age-related macular degeneration (wAMD) patients and controls. Methods: Blood samples were obtained from 60 Finnish wAMD patients and 64 controls. After serum preparation and RNA sequencing, the count data was examined for differentially expressed genes (DEGs) and further checked for enriched molecular pathways and ontology terms as well as links to clinical data. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

124 Samples

Download data: TXT

(Submitter supplied) Human brown and white adipocytes (hBAT and hWAT) display markedly distinct m6A landscapes; besides, in insulin-resistant humans and mice, methyltransferase like 14 (METTL14) expression differs significantly between BAT and WAT in the context of its correlation with insulin sensitivity. We therefore employed independent BAT- and WAT-specific METTL14 knockout models to unveil the cell-type specificity of m6A mRNA methylation. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

58 Samples

Download data: CSV

(Submitter supplied) In the lungs of chronic obstructive pulmonary disease (COPD) patients, numerous cell types interact in a structurally abnormal and inflammatory microenvironment. Assessing gene expression in individual cells by single-cell RNA sequencing (scRNA-seq) allows for a deeper understanding of cell types within a complex sample, like the COPD distal lung. ScRNA-seq data can be combined with cell-cell communication prediction tools to predict cellular interactions within a given sample; indeed, this approach was previously used to show evidence for increased endothelial CXCL signaling in COPD. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: MTX, TSV

(Submitter supplied) Trained immunity is a phenomenon where innate immune cells develop and long-lasting pro-inflammatory reprogramming mediated by epigenetic and metabolic reprogramming. Trained immunity can be peropheral (circulating monocytes) or central (bone marrow) and it can be caused by exposure to β-glucan, BCG and Western Type Diet vial IL-1β signaling.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

12 Samples

Download data: COUNTS

(Submitter supplied) The prevalence of lung adenocarcinoma (LUAD) has increased sharply in East Asia. Early diagnosis leads to better survival rates, but this requires an improved understanding of the molecular changes during early tumorigenesis, particularly in non-smokers. We performed whole exome-sequencing and RNA-sequencing of samples from 94 East Asian patients with precancerous lesions (25 with atypical adenomatous hyperplasia [AAH]; 69 with adenocarcinoma in situ [AIS]) and 73 patients with early invasive lesions (minimally invasive adenocarcinoma [MIA]). more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

2 Samples

Download data: H5

(Submitter supplied) RNA-Seq analysis was carried out to investigate the transcriptomic changes associated with the development of in vivo everolimus resistance and the effects of CDK8/19 inhibition on the development of resistance in MDA-MB-468 TNBC xenografts. In one study (short-term), tumor samples were collected after 30-40 days of treatment with vehicle or everolimus, when the tumor growth was still suppressed by the mTOR inhibitor. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

50 Samples

Download data: TXT

(Submitter supplied) Background: Diabetic kidney disease (DKD) is the leading cause of end-stage renal disease worldwide with limited treatment options. The intricate pathogenesis of dysregulated lipid metabolism leading to the development of DKD remains obscure. Lipophagy, which refers to the autophagic degradation of intracellular lipid droplets, has been found to be impaired in DKD, resulting in renal tubule dysfunction and ectopic lipid deposition (ELD). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Difference in salt concentration may cause dramatic alterations in tumor microenvironment, progression of cancer and overall outcome of cancer therapy. Immune cells in tumor microenvironment are mostly immunosuppressed under the influence of tumor cells. Recent studies has shown that high salt induces immune cells to pro-inflammatory state in the tumor microenvironment. On contrary, it hinders the immunosuppressive functions of regulatory T cells, which plays an important role in inhibiting anti-cancer immune responses in tumor microenvironment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array; Methylation profiling by high throughput sequencing

Platforms:

GPL28271 GPL17021

283 Samples

Download data: IDAT

(Submitter supplied) We identified widespread DNA methylation changes associated with the development of both tau and amyloid neuropathology, including differentially methylated positions (DMPs) and regions (DMRs) at loci previously implicated in AD and overlapping changes identified in our ongoing analyses of human post-mortem AD brains.

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

159 Samples

Download data: CSV, IDAT

(Submitter supplied) We report the transcriptome profiles of A375 melanoma tumors containing distinct mtDNA mutations. This study was performed using subcutaneous tumors implanted into NSG mice, and identifies transcriptomice changes in response to pathogenic mtDNA mutations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

13 Samples

Download data: XLSX

(Submitter supplied) m6A mRNA methylation in brown adipose tissue regulates systemic insulin sensitivity. We performed N6-methyladenosine (m6A) profiling and RNA seq of brown adipose tissue (BAT) from control and Mettl14-KO mice. Meanwhile, we performed RNA-seq for control and Mettl14-KO human BAT cell line as well.

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

21 Samples

Download data: CSV

(Submitter supplied) Growing evidence suggests an increased prevalence of nonalcoholic fatty liver disease (NAFLD) in the context of immune-mediated inflammatory diseases (IMIDs). We aimed to clinically and mechanistically characterize a prospective cohort of IMID-NAFLD patients compared to classic-NAFLD patients.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

109 Samples

Download data: XLSX

(Submitter supplied) We established an immortalized term placenta-derived trophoblast cell line and demonstrated functional and transcriptomic differences against chorion trophoblasts and BeWo cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

31 Samples

Download data: TXT

(Submitter supplied) Copper (Cu) is an essential trace element required for mitochondrial respiration. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis and promotes tumor growth and progression of clear cell renal cell carcinoma (ccRCC). Late-stage ccRCCs accumulate Cu and allocate it to cytochrome c oxidase stimulating bioenergy production. Cu induces TCA cycle-dependent oxidation of glucose and its utilization for biosynthesis of a glutathione pool that protects against H2O2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

5 Samples

Download data: CSV, H5, JPG, JSON, MTX, PNG, TSV

(Submitter supplied) Tumors acquire an increased ability to obtain and metabolize nutrients. Here, we engineered adipocytes to outcompete tumors for nutrients and show that they can substantially reduce cancer progression. Growing cells from several cancers (breast, colon, pancreas, prostate) with engineered human adipocytes or xenografts alongside adipose organoids significantly suppresses cancer progression and reduces hypoxia and angiogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

17 Samples

Download data: TXT

(Submitter supplied) In preclinical experiments, cyclic fasting-mimicking diets (FMDs) showed broad anticancer effects in combination with chemotherapy. Among different tumor types, triple-negative breast cancer (TNBC) is exquisitely sensitive to FMD. However, the antitumor activity and efficacy of cyclic FMD in TNBC patients remain unclear. Here, we show that a severely calorie-restricted, triweekly, 5-day FMD regimen results in excellent pathologic complete response (pCR) rates (primary endpoint) and long-term clinical outcomes (secondary endpoints) when combined with preoperative chemotherapy in 30 patients with early-stage TNBC enrolled in the phase II trial BREAKFAST. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

24 Samples

Download data: MTX, TSV