GEO DataSets

(Submitter supplied) In human EndoCβH5 cells, i.e. post-mitotic mature pancreatic beta cells that endogenously express OPRD1 encoding delta opioid receptor (transcripts per million [TPM] of 11 according to our RNA-seq data), a specific antagonist for delta opioid receptor (naltrindole [NTI]) significantly increased insulin secretion in high glucose condition. We performed RNA-seq in these cells to decipher signalling pathways under delta opioid receptor antagonism.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: RESULTS, TSV

(Submitter supplied) Age-induced decline in osteogenic potential of bone marrow mesenchymal stem cells (BMSCs) potentiates osteoporosis and increases risk for bone fractures. Despite epidemiology studies reporting concurrent development of vascular- and bone diseases in the elderly, the underlying mechanisms for the vascular-bone cross-talk in aging are largely unknown. In this study, we show that accelerated endothelial aging deteriorates bone tissue through paracrine repression of Wnt-driven-axis in BMSCs. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: CSV

(Submitter supplied) Dopaminylation, the covalent attachment of dopamine to the side chain of glutamine (Gln, Q) in proteins, has been identified as a class of posttranslational modification. Due to the limited number of substrates, the functions and underlying molecular mechanisms of dopaminylation are not fully characterized. Utilizing an alkyne-functionalized dopamine probe, we have developed a method to selectively enrich dopaminylated proteins in the whole-cell context. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29480

4 Samples

Download data: BIGWIG

(Submitter supplied) The OP9 coculture system is widely used to differentiate pluripotent stem cells into mesodermal lineages. We used single cell RNA sequencing to analyze differentiation trajectories and heterogeniety of differentiating pluripotent stem cells using the OP9 coculture system.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: CLOUPE

(Submitter supplied) Transcriptional profiling of the antennae of adult honeybee workers with a dsx stop/stop mutation and wild-type workers was performed by RNA-Seq. Gene expression of the dsx stop/stop and wild type female workers was compared.

Organism:

Apis mellifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34623

6 Samples

Download data: TXT

(Submitter supplied) Folate is crucial for diverse biological processes including neurogenesis. While folate supplementation during pregnancy is standard for preventing neural tube defects (NTDs), concerns are growing over the potential risks of excessive maternal intake. In this study, we employed spatial transcriptomics and single-nucleus multi-omics techniques to investigate the impact of increased maternal folate intake on offspring brain development. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL24247

8 Samples

Download data: MTX, TSV

(Submitter supplied) Folate is crucial for diverse biological processes including neurogenesis. While folate supplementation during pregnancy is standard for preventing neural tube defects (NTDs), concerns are growing over the potential risks of excessive maternal intake. In this study, we employed spatial transcriptomics and single-nucleus multi-omics techniques to investigate the impact of increased maternal folate intake on offspring brain development. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

4 Samples

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

(Submitter supplied) Increased plasma uric acid (hyperuricemia) has been associated with worse outcomes for chronic kidney disease (CKD). But some attempts to control uric acid (UA) in large-cohort clinical trials did not produce clinically meaningful benefits for CKD. Some studies suggest that only hyperuricemia with crystals, but not asymptomatic hyperuricemia promotes the progression of CKD. Salt-sensitivity (SS) in blood pressure is a prevalent trait that is sexually dimorphic and results in kidney damage. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

10 Samples

Download data: TXT

(Submitter supplied) This dataset contains RNA-seq results from rat embryonic striatal neuronal cultures treated with CRISPRi machinery (dCas9-KRAB-MeCP2 fusion) with a CRISPR sgRNA targeting lacZ (a bacterial gene not found in the mammalian genome; used as a non-targeting control) or Reln.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

8 Samples

Download data: TXT

(Submitter supplied) More than 90% of hepatocellular carcinoma (HCC) cases develop in the presence of fibrosis or cirrhosis, making the tumor microenvironment (TME) of HCC distinctive due to the intricate interplay between cancer-associated fibroblasts (CAFs) and cancer stem cells (CSCs), which collectively regulate HCC progression. However, the mechanisms through which CSCs orchestrate the dynamics of the tumor stroma during HCC development remain elusive. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Despite lower rates and intensity of smoking, Black men experience a higher incidence of lung cancer compared to White men. The racial disparity in lung cancer is particularly pronounced in Chicago, a highly segregated urban city. Neighborhood conditions, particularly social stress, may play a role in lung tumorigenesis. Preliminary studies indicate that Black men residing in neighborhoods with higher rates of violent crime have significantly higher levels of hair cortisol, an indicator of stress response. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

15 Samples

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

(Submitter supplied) Despite lower rates and intensity of smoking, Black men experience a higher incidence of lung cancer compared to White men. The racial disparity in lung cancer is particularly pronounced in Chicago, a highly segregated urban city. Neighborhood conditions, particularly social stress, may play a role in lung tumorigenesis. Preliminary studies indicate that Black men residing in neighborhoods with higher rates of violent crime have significantly higher levels of hair cortisol, an indicator of stress response. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

55 Samples

Download data: BED, TXT

(Submitter supplied) We reported the RNAseq analyses of pulmonary vein tissues at the age of postnatal day 21 (P21) on SD rats with or without pulmonary vein stenosis. Pulmonary vein stenosis was induced by performing pulmonary vein banding surgery within 24 hours postnatally. RNAseq analyses of the pulmonary vein tissues was generated at P21 from 3 sham-operated rats and 3 pulmonary vein banding rats. The results revealed that there were 1124 differentially expressed genes between PAB and sham group at P7, among which 714 were upregulated and 410 were downregulated.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25947

6 Samples

Download data: TXT

(Submitter supplied) To further investigate gene expression in DEN-induced liver cancer in mice with Otud3 gene knockout, we employed RNA-seq profiling as a discovery platform to identify the pathways or biological processes potentially responsible for the occurrence of DEN-induced liver cancer in both wildtype and Otud3 knockout mice. Liver cancer tissues from Otud3 knockout mice and their littermates, with or without a 14-day-old DEN injection, were utilized as samples for analysis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28457

12 Samples

Download data: TXT

(Submitter supplied) Aim To identify transcript level differences between healthy and osteoarthritis meniscus in human keen joint using RNA-seq.Methods human menisci were isolated from non-OA patients and OA patients during arthroscopic surgery (N=5). Based on the RNA sequencing, differentially expressed lncRNAs (DELs) and mRNAs (DEMs) were screened.Expression level of selected autophagy-related lncRNAs and mRNAs was validated by real-time qPCR.Results we identified 310 DELs and 320 DEMs, and found five upregulated and one downregulated autophagy-related DEMs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

10 Samples

Download data: TXT

(Submitter supplied) The increasing global burden of metabolic disorders including obesity and diabetes necessitates a comprehensive understanding of their etiology, which not only encompasses genetic and environmental factors but also parental influence. Recent evidence has unveiled paternal obesity as a contributing factor to offspring's metabolic health via sperm epigenetic modifications. In this study, we investigated the impact of a Western diet-induced obesity in C57BL/6 male mice on sperm chromatin accessibility and the subsequent metabolic health of their progeny. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30172

10 Samples

Download data: NARROWPEAK

(Submitter supplied) Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: BW, TXT

(Submitter supplied) Lamina-associated domains (LADs) are large chromatin regions that are associated with the nuclear lamina and form a repressive environment for transcription. The molecular players that mediate gene repression in LADs are currently unknown. Here we performed a full-genome genetic screen in human cells using LAD-integrated fluorescent reporters to identify such regulators. Surprisingly, the screen identified very few lamina proteins, but revealed roles for dozens of known chromatin regulators. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL16791

14 Samples

Download data: BW

(Submitter supplied) Tumor resistance to immune cells remains a major obstacle for successful treatment. NK cells are emerging tools for cancer therapy. However, due to differential and subset-specific expression of inhibitory NK cell receptors, often only subsets of NK cells exert reactivity against particular cancer types. Using a genome-wide CRISPR/Cas9 knockout (KO) screen in melanoma, we revealed resistance factors against NK cell attack and evaluated their differential impact on NK cell subpopulations. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

3 Samples

Download data: TXT

(Submitter supplied) Pseudouridine (Ψ), the isomer of uridine, is ubiquitous in most RNA families, including tRNA, rRNA and mRNA. Pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs, but whether it can modify other RNA types, including mRNA, remains elusive. Here, we determine the single particle cryo-EM structure of apo and tRNA-bound human PUS3, showing how it forms a symmetric homodimer that recognizes the characteristic L-shape of tRNA across two distinct interaction interfaces. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

36 Samples

Download data: TXT