GEO DataSets

(Submitter supplied) Circulating microRNAs are linked to the onset and progression of type 1 diabetes mellitus (T1DM), making them potential biomarkers for the disease. In this study, we employ a multiplatform sequencing approach to analyze circulating microRNAs in an extended cohort of individuals with T1DM from the INNODIA consortium. Our findings reveal that a set of microRNAs located within the T1DM susceptibility chromosomal locus 14q32 distinguishes two subgroups of individuals. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

154 Samples

Download data: CSV

(Submitter supplied) Circulating microRNAs are linked to the onset and progression of type 1 diabetes mellitus (T1DM), making them potential biomarkers for the disease. In this study, we employ a multiplatform sequencing approach to analyze circulating microRNAs in an extended cohort of individuals with T1DM from the INNODIA consortium. Our findings reveal that a set of microRNAs located within the T1DM susceptibility chromosomal locus 14q32 distinguishes two subgroups of individuals. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24676

121 Samples

Download data: CSV

(Submitter supplied) Circulating microRNAs are linked to the onset and progression of type 1 diabetes mellitus (T1DM), making them potential biomarkers for the disease. In this study, we employ a multiplatform sequencing approach to analyze circulating microRNAs in an extended cohort of individuals with T1DM from the INNODIA consortium. Our findings reveal that a set of microRNAs located within the T1DM susceptibility chromosomal locus 14q32 distinguishes two subgroups of individuals. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

119 Samples

Download data: CSV

(Submitter supplied) Exposure to persistent organic pollutants (POPs), such as dichlorodiphenyltrichloroethane (DDT) and polychlorinated biphenyls (PCBs), has historically been linked to population collapses in wildlife. Despite international regulations, these legacy chemicals are still currently detected in women of reproductive age, and their levels correlate with reduced ovarian reserve, longer time-to-pregnancy, and higher risk of infertility. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

242 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL30173

217 Samples

Download data: TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

216 Samples

Download data

(Submitter supplied) A subset of patients with IDH-mutant glioma respond to inhibitors of mutant IDH (IDHi), yet the molecular underpinnings of such responses are not understood. Here, we profiled by single-cell or single-nucleus RNA-sequencing three IDH-mutant oligodendrogliomas from patients who derived clinical benefit from IDHi. Importantly, the tissues were sampled on-drug, four weeks from treatment initiation. We further integrate our findings with analysis of single-cell and bulk transcriptomes from independent cohorts and experimental models. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30172

141 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

6 related Platforms

168 Samples

Download data: BED, IDAT, MTX, TSV, TXT

(Submitter supplied) Eukaryotic DNA fibers are organized into structured subunits in the nucleus, but the extent to which these 3D chromatin architectures influence cytokine expression remains unclear. Here, we investigate the role of dynamic loop formation within the topologically associating domain (TAD) in regulating the expression of two critical cytokines, interferon-gamma (IFN-) and interleukin-22 (IL-22). These cytokine loci are closely located in the genome and are associated with complex enhancer landscapes, which are selectively active in type 1 and type 3 lymphocytes. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL24247 GPL21626

135 Samples

Download data: BW, H5, HIC, TXT

(Submitter supplied) Principle of tumor growth is one fundamental aspect of cancer biology and it remains to be superficially understood. Here we developed a set of genetic and mathematic tools allow integrative analysis of mouse glioblastoma (GBM) progression. Quantitative temporal imaging of mouse GBM and mathematic modeling suggest that mouse GBM grows exponentially, which led to the discovery that a sustainable exponential growth requires outward migrating brain tumor stem cells (BTSCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

152 Samples

Download data: TXT

(Submitter supplied) Samul-tang (SM) is a traditional multi-ingredient treatment widely used in clinical practice for improving ovarian function in women with diminished ovarian reserve. Despite its therapeutic benefits, the complexity of its mechanisms of action due to the combination of multiple compounds has limited its research integration into modern pharmacological science. To address this challenge, we identified 39 herbal compounds as major ingredients in SM and generated transcriptome data from the mice ovaries after administrating with individual ingredients. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

127 Samples

Download data: RESULTS

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

Organism:

Mus musculus; Homo sapiens

Type:

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

Platforms:

GPL24676 GPL24247 GPL18573

127 Samples

Download data: COV

(Submitter supplied) In this study 14 different RAF, MEK, or ERK inhibitors were tested in ASPC1 and PANC1 PDA cell lines

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

152 Samples

Download data: CSV

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

Organism:

Brassica napus; Glycine max; Populus; Solanum tuberosum; Oryza sativa; Saccharum officinarum; Citrus sinensis; Zea mays; Dianthus caryophyllus; Arabidopsis thaliana; Solanum lycopersicum

Type:

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

11 related Platforms

160 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. more...

Organism:

Arabidopsis thaliana; Brassica napus; Solanum tuberosum; Saccharum officinarum; Citrus sinensis; Populus; Oryza sativa; Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

152 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Enzymes catalyze the reactions of life and are the targets of nearly all small molecule drugs. Most drugs inhibit enzymes by binding to conserved active sites, causing problems of specificity and toxicity. Targeting regulatory allosteric sites can increase specificity, overcome drug resistance and tune or activate activity.However, the vast majority of enzymes have no known allosteric sites and methods do not exist to globally identify or predict them.Here we present a general and fast method to globally chart allosteric communication in enzymes and apply it to the Src protein kinase to produce the first comprehensive map of negative and positive allosteric control of enzymatic activity. more...

Organism:

Homo sapiens; Saccharomyces cerevisiae

Type:

Other

Platform:

GPL33934

118 Samples

Download data: TXT

(Submitter supplied) Stress-induced condensation of mRNA and proteins into stress granules is conserved across eukaryotes, yet the function, formation mechanisms, and relation to well-studied conserved transcriptional responses remain largely unresolved. Stress-induced exposure of ribosome-free mRNA following translational shutoff is thought to cause condensation by allowing new multivalent RNA-dependent interactions, with RNA length and associated interaction capacity driving increased condensation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL27812 GPL21656

279 Samples

Download data: CSV, FASTA, GFF, GFF3, TSV

(Submitter supplied) Natural killer-like B (NKB) cells are unique innate immune cells that express both natural killer (NK) and B cell markers. They act as first responders by secreting IL-18 upon infection, thus inducing the critical cascade of innate and adaptive immune cell infiltration and activation. However, limited research exists on the role of NKB cells in homeostasis, and infection in primates. Therefore, we investigated the signaling and trafficking proteome, in situ localization and transcriptome of NKB cells in comparison to conventionally defined NK and B cells. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27943

314 Samples

Download data: TXT

(Submitter supplied) Meningiomas are the most common primary intracranial tumors in humans. While most of these tumors are benign, some are malignant, rapidly recur after multimodal treatment with surgery and radiotherapy, and can ultimately be fatal. The current WHO grade system does not always identify high risk meningiomas, therefore better characterizations of the biology of aggressive tumors are needed. In order to address these challenges, we combined 13 bulk RNA-Seq datasets, corrected for batch effects, and applied Uniform Manifold Approximation and Projection (UMAP) to create a reference landscape of ~1300 meningioma tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

279 Samples

Download data: TXT

(Submitter supplied) Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging. We performed single-cell RNA sequencing (scRNA-seq) of treatment-naive primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

218 Samples

Download data: TXT