GEO DataSets

(Submitter supplied) NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL21697

22 Samples

Download data: TXT

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19057 GPL18573

32 Samples

Download data

(Submitter supplied) Although altered TRAF6 expression is observed in human acute myeloid leukemia (AML), its role in the AML pathogenesis remains elusive. In this study, we showed that the loss of TRAF6 in AML cells significantly impairs leukemic function in vitro and in vivo, indicating its functional importance in AML subsets. Loss of TRAF6 induces metabolic alterations, such as changes in glycolysis as well as impaired mitochondrial membrane potential and respiratory capacity. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL18573

24 Samples

Download data: XLSX

(Submitter supplied) The underlying causes of breast cancer are diverse, however, there is a striking association between type 2 diabetes (T2DM) and poor patient outcomes. Platelets become activated in both T2DM and breast cancer patients and have been implicated in tumorigenesis through a multitude of pathways. Here transcriptomic analysis of T2DM-patient derived PMVs revealed an altered micro-RNA (miRNA) signature compared with normoglycaemic control patients. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

10 Samples

Download data: TXT

(Submitter supplied) Remarkable advancements in protocol development have been achieved to manufacture insulin-secreting islets from human pluripotent stem cells. Distinct from current approaches, we devised a tunable strategy to generate islet spheroids enriched for major islet cell types by incorporating PDX1+ cell budding morphogenesis into the differentiation process of staged transcriptional programming. In this process that appears to mimic normal islet morphogenesis, the differentiating islet spheroids self-organize with endocrine cells that are intermingled or arranged in a core-mantle architecture, accompanied with functional heterogeneity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT

(Submitter supplied) Neutrophils, a major innate immune cell population, are the most abundant circulating white blood cell in humans. They play a crucial role in host defense against infection; however, aberrant neutrophil activation may induce tissue damage via sterile inflammation. Neutrophil accumulation has been identified as a feature of the inflammatory response observed MASH and has been associated with liver fibrosis and cirrhosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) Biliary atresia (BA) is an devastating pediatric cholangiopathy and the leading indication for liver transplant in children worldwide. An in vitro cell system for investigating BA is still lacking. We develop an in vitro cell culture system to mimic immune dysfunction of biliary atresia by coculturing human peripheral blood mononuclear cells (PBMC) with rotavirus treated or PBS treated human cholangiocyte cell line H69. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: MTX, TSV

(Submitter supplied) Heritable gene silencing is essential for the development of multicellular organisms. Polycomb repressive complexes 1 and 2 (PRC1 and 2) catalyze and recognize histone H2A lysine 119 mono-ubiquitination (H2AK119ub1) and histone H3 lysine 27 trimethylation (H3K27me3), respectively, to mediate heritable gene silencing, but the mechanism of inheritance is not fully understood. Using an inducible gene silencing strategy, we show that the epigenetic inheritance of Polycomb silencing in human cells is strongly dependent on local DNA sequences and chromatin environment. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

48 Samples

Download data: BW, FASTA

(Submitter supplied) Background: Mesenchymal stromal/stem cells (MSC) can enhance the neovascularization processes required for wound healing and are widely used as an autologous source of progenitor cells in stem cell-based therapies. However, incomplete MSC differentiation towards a vascular endothelial cell phenotype questions their involvement in an alternative process to angiogenesis, namely vasculogenic mimicry (VM), and the signal transducing events that regulate their in vitro priming into 3D capillary-like structures. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: TXT

(Submitter supplied) RNA constitutes a large fraction of chromatin. Spatial distribution and functional relevance of most of RNA interactions within the chromatin remain unknown. We established a landscape analysis of RNA-chromatin interactions in human acute myeloid leukemia (AML). In total more than 50 million interactions were captured in an AML cell line. Protein-coding mRNAs and long non-coding RNAs (lncRNAs) exhibited a substantial number of interactions with chromatin in cis suggesting transcriptional activity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

18 Samples

Download data: BW

(Submitter supplied) RNA constitutes a large fraction of chromatin. Spatial distribution and functional relevance of most of RNA interactions within the chromatin remain unknown. We established a landscape analysis of RNA-chromatin interactions in human acute myeloid leukemia (AML). In total more than 50 million interactions were captured in an AML cell line. Protein-coding mRNAs and long non-coding RNAs (lncRNAs) exhibited a substantial number of interactions with chromatin in cis suggesting transcriptional activity. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

4 Samples

Download data: PAIRS

(Submitter supplied) RNA constitutes a large fraction of chromatin. Spatial distribution and functional relevance of most of RNA interactions within the chromatin remain unknown. We established a landscape analysis of RNA-chromatin interactions in human acute myeloid leukemia (AML). In total more than 50 million interactions were captured in an AML cell line. Protein-coding mRNAs and long non-coding RNAs (lncRNAs) exhibited a substantial number of interactions with chromatin in cis suggesting transcriptional activity. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

4 Samples

Download data: BW

(Submitter supplied) RNA constitutes a large fraction of chromatin. Spatial distribution and functional relevance of most of RNA interactions within the chromatin remain unknown. We established a landscape analysis of RNA-chromatin interactions in human acute myeloid leukemia (AML). In total more than 50 million interactions were captured in an AML cell line. Protein-coding mRNAs and long non-coding RNAs (lncRNAs) exhibited a substantial number of interactions with chromatin in cis suggesting transcriptional activity. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BW

(Submitter supplied) Screening for dysregulated mirnas in serum exosomes in patients with osteoarthritis compared to healthy individuals.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

25 Samples

Download data: XLSX

(Submitter supplied) Triple-negative breast cancer (TNBC) stands out as a particularly aggressive and frequently recurring form of breast cancer. Due to the absence of hormone receptors, the available treatment avenues are constrained, making chemotherapy the primary approach. Unfortunately, the development of resistance to chemotherapy poses a significant challenge, further restricting the already limited therapeutic alternatives for recurrent cases. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL23227

27 Samples

Download data: TXT

(Submitter supplied) We discovered a novel small-molecule TERT activating compound (TAC) that selectively enhances TERT transcription in human and mouse adult somatic cells. Our findings also provide the novel mechanism of TAC-mediated TERT up-regulation and elucidate the impact of TERT induction on regulatory factors governing aging.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: BW

(Submitter supplied) High-throughput phenotypic screens leveraging biochemical perturbations and high-content readouts are poised to advance therapeutic discovery, yet they remain constrained by limitations of scale. To address this, we establish a method of pooling exogenous perturbations followed by computational deconvolution to compress a screen’s required sample, labor, and financial input. We benchmark the approach with a bioactive small molecule library and a high-content imaging readout, demonstrating the feasibility and increased efficiency of compressed experimental designs compared to conventional approaches. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

54 Samples

Download data: MTX, TSV

(Submitter supplied) An effective long-term inhibition of multiple DNA repair signals is required to design a novel and effective therapeutic for glioblastoma (GBM), a highly DNA repair ‘addicted’ cancer. AsiDNA, a double-strand DNA break (DSB) mimetic, is an innovative approach that shuts down the entire DNA repair system in cancer cells by sequestering DSB repair factors. We showed that inhibition of class I histone deacetylases (HDACs) dislodges repair factors from sites of DNA damage. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

16 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Heme, an iron-containing tetrapyrrole, serves physiological functions as a prosthetic group of various hemoproteins. By contrast, excess free heme that is not bound to proteins can be harmful via its pro-oxidant and cytotoxic effects. In macrophages, heme appears to induce both- pro- and anti-inflammatory activation but the underlying mechanisms are not well understood. Here, we compared the response of human blood-monocyte derived macrophages (hMDMs) and mouse bone-marrow derived macrophages (mBMDMs) to heme and the Toll-like receptor (TLR)4 ligand lipopolysaccharide (LPS), particularly focusing on how energetic metabolism is modulated in these two cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 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:

GPL18573

28 Samples

Download data: TXT