GEO DataSets

(Submitter supplied) To understand the common and opposite effects of mitochondrial and lysosomal perturbations on cellular signaling, we performed RNAseq in HeLa cells stably silenced for the mitochondrial respiratory chain subunit UQCRC1 (as a model of chronic mitochondrial respiratory chain deficiency), for lysosomal hydrolase acid alpla-glucosidase (GAA), or for lysosomal cathepsin B (CTSB). The controls were HeLa cells with scrambled shRNA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

10 Samples

Download data: XLSX

(Submitter supplied) Embryonic stem cells (ESCs) are defined as stem cells with self-renewing and differentiation capabilities. These unique properties are tightly regulated and controlled by complex genetic and molecular mechanisms whose understanding is essential for both basic and translational research. A large number of existing studies in the broader literature have mostly focused on understanding the molecular mechanisms governing pluripotency and differentiation of ESCs, while the regulation of proliferation has received comparably less attention. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

12 Samples

Download data: TXT

(Submitter supplied) The packaging of DNA into chromatin and its compaction within cells renders the underlying DNA template un-accessible for processes like transcription, replication and repair. Active mechanisms as chromatin modifying activities or the association with non-coding RNAs can de-condense chromatin, rendering it accessible for the DNA dependent processes. High mobility group proteins (HMG) are small architectural chromatin proteins that were shown to contribute to the regulation of chromatin accessibility and condensation. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL15433

13 Samples

Download data

(Submitter supplied) HMGN5 is a member of the HMGN family that de-compacts chromatin and regulates gene expression. Chromatin-associated RNAs are known to play a major role in controlling gene expression and chromatin architecture. We recently showed that RNA is required to open chromatin structure in Drosophila. A potential involvement of RNA in the HMGN5-dependent opening of chromatin has not been studied so far. Here we revealed that HMGN5 has a novel and specific RNA binding activity, which is extended to the HMGN family. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

5 Samples

Download data: TXT

(Submitter supplied) HMGN5 is a member of the HMGN family that de-compacts chromatin and regulates gene expression. Chromatin-associated RNAs are known to play a major role in controlling gene expression and chromatin architecture. We recently showed that RNA is required to open chromatin structure in Drosophila. A potential involvement of RNA in the HMGN5-dependent opening of chromatin has not been studied so far. Here we revealed that HMGN5 has a novel and specific RNA binding activity, which is extended to the HMGN family. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15433

5 Samples

Download data: TXT

(Submitter supplied) In adoptive T cell therapy, the long term therapeutic benefits in patients treated with engineered tumor specific T cells are limited by the lack of long term persistence of the infused cellular products and by the immunosuppressive mechanisms active in the tumor microenvironment. Exhausted T cells infiltrating the tumor are characterized by loss of effector functions triggered by multiple inhibitory receptors (IRs). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

22 Samples

Download data: TXT

(Submitter supplied) Post mortem brain tissue of three Patients suffering from Aicardi-Goutières Syndrome from different brain regions was used to isolate RNA and perform RNAseq analysis compared to age matched control patients with no underlying brain pathology.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

18 Samples

Download data: TSV

(Submitter supplied) To investigate mechanisms underlying frequent asthma exacerbation, we profiled the nasal transcriptome of both frequent and non-frequent asthma exacerbators.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

139 Samples

Download data: CSV

(Submitter supplied) Microglia and neuroinflammation are implicated in the development and progression of Alzheimer’s disease (AD). To better understand microglia-mediated processes in AD, we studied the function of INPP5D/SHIP1, a gene linked to AD through GWAS. Immunostaining and single nucleus RNA sequencing confirmed that INPP5D expression in the adult human brain is enriched in microglia. Examination of prefrontal cortex across a large cohort revealed reduced full-length soluble INPP5D protein levels in AD patient brains compared to cognitively normal controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

28 Samples

Download data: CSV

(Submitter supplied) Acute exposure to high-dose gamma radiation can result in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip lined by human lung alveolar epithelium interfaced with pulmonary endothelium (Lung Alveolus Chip) is used to model acute, early stage RILI in vitro. Both lung epithelium and endothelium exhibit DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6h of radiation exposure, and greater damage is observed in the endothelium. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

32 Samples

Download data: TXT

(Submitter supplied) Acute exposure to high-dose gamma radiation often results in radiation-induced lung injury (RILI), characterized by acute pneumonitis and subsequent lung fibrosis. A microfluidic organ-on-a-chip device consisting of human lung alveolar epithelium and pulmonary endothelium (Lung Alveolus Chip) is used to recapitulate acute, early stage RILI in vitro. This RNA-seq data captures that both the lung epithelium and endothelium in this model capture key hallmarks of this disease particularly, DNA damage, cellular hypertrophy, upregulation of inflammatory cytokines, and loss of barrier function within 6h of radiation exposure. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

24 Samples

Download data: TXT

(Submitter supplied) Esophageal squamous cell carcinoma (ESCC) immunotherapy exhibits limited efficacy, prompting the investigation of its molecular mechanisms. Circular RNAs (circRNAs) are believed to play a significant role in the development of the tumor microenvironment (TME) in ESCC, but their role in ceRNA regulation remains indeterminate. In this study, we identified the expression of mRNA, circRNA in four tumor samples and their pair normal samples noting their paired samples by high-throughput sequencing to validate the correlation analysis.

Organism:

Homo sapiens

Type:

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

Platform:

GPL15433

8 Samples

Download data: XLSX

(Submitter supplied) To comprehensively characterize MAIT activation programs responding to different bacteria, we stimulated MAIT cells with E. coli to compare with Bacillus Calmette-Guérin (BCG), which remains the only licensed vaccine and a feasible tool for investigating anti-mycobacterial immunity in humans. Upon sequencing mRNA from the activated and inactivated CD8+ MAIT cells, results demonstrated the altered MAIT cell gene profiles by each bacterium with upregulated expression of activation markers, transcription factors, cytokines, and cytolytic mediators crucial in anti-mycobacterial responses.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

9 Samples

Download data: XLSX

(Submitter supplied) Exosomes are nano-sized (30-150 nm), membrane encapsulated vesicles that are released by cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA). Although secreted by both normal and malignant cells, there is evidence that cancer-derived exosomes enable the tumor to manipulate its microenvironment, contributing to the capacity of the tumor for immune evasion, growth, invasion, and metastatic spread. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15433

15 Samples

Download data: CSV

(Submitter supplied) Exosomes are nano-sized (30-150 nm), membrane encapsulated vesicles that are released by cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA). Although secreted by both normal and malignant cells, there is evidence that cancer-derived exosomes enable the tumor to manipulate its microenvironment, contributing to the capacity of the tumor for immune evasion, growth, invasion, and metastatic spread. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15433

32 Samples

Download data: XLSX

(Submitter supplied) In previous study, we found circFAT1(e2) was highly expressed in breast cancer tissues and cell lines. And this factor is also a crucial role in breast cancer genesis and development. So in this study, we knocked down circFAT1(e2) in MCF-7 cells. The viability and metastasis was significantly inhibited with circFAT1(e2) depletion. In order to explore the potential down-stream gene of circFAT1(e2) in breast cancer cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

6 Samples

Download data: XLSX

(Submitter supplied) This experiment seeks to identify differences in human proximal tubule cells in 2D and 3D in response to nephrotoxins, identify early indications to predict toxicity

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

44 Samples

Download data: XLSX

(Submitter supplied) Acute myeloid leukaemia (AML) is a heterogeneous haematological malignancy caused by mutations in genes encoding transcriptional and epigenetic regulators together with signalling genes. It is characterised by a disturbance of differentiation and abnormal proliferation of hematopoietic progenitors. We have previously shown that each AML subtype establishes its own core gene regulatory network, consisting of transcription factors binding to their target genes and imposing a specific gene expression pattern that is required for AML maintenance. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL15433

1 Sample

Download data: BED

(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; Other

Platforms:

GPL18573 GPL15433

42 Samples

Download data: BED, BEDGRAPH, H5, TSV

(Submitter supplied) To investigate the role of tight junctions in BMP4 signaling and differentiation, we knocked down TJP1 in human pluripotent stem cells using CRISPRi, and examined gene expression via RNA sequencing of TWT (no KD) and TKD (TJP1 KD) cells in the untreated pluripotent (P) state and after BMP4 differentiation (B).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15433 GPL24676

24 Samples

Download data: CSV