GEO DataSets

(Submitter supplied) Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by the death of upper and lower motor neurons with unknown etiology. The difficulty to recover biological material from patients led to employ lymphoblastoid cell lines (LCLs) as a model for ALS, since many pathways, typically located in neurons, are also activated in these cells. To investigate the expression of coding and long noncoding RNAs in LCLs, a transcriptomic profiling of Sporadic ALS (SALS) and mutated patients (FUS, TARDBP, C9ORF72 and SOD1), and matched controls was realized. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15433

20 Samples

Download data: RESULTS

(Submitter supplied) Twenty healthy subjects (25±5yrs) completed two high-intensity interval training interventions (training and retraining) lasting 8 weeks separated by 12 weeks of detraining. Measurements at baseline and after training, detraining and retraining included maximal oxygen consumption (V̇O2max), along with vastus lateralis biopsy for genome wide DNA methylation using Illumina Epic arrays in 5 of the participants for all conditions (baseline, training, detraining and retraining).

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

20 Samples

Download data: IDAT, TXT

(Submitter supplied) Splicing factor SF3B1 mutations are frequent somatic lesions in myeloid neoplasms that transform hematopoietic stem cells (HSCs) by inducing mis-splicing of target genes. However, the molecular and functional consequences of SF3B1 mutations in human HSCs remain unclear. Here, we identify the mis-splicing program in human HSCs as a targetable vulnerability by precise gene editing of SF3B1 K700E mutations in primary CD34+ cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

2 Samples

Download data: H5AD

(Submitter supplied) Splicing factor SF3B1 mutations are frequent somatic lesions in myeloid neoplasms that transform hematopoietic stem cells (HSCs) by inducing mis-splicing of target genes. However, the molecular and functional consequences of SF3B1 mutations in human HSCs remain unclear. Here, we identify the mis-splicing program in human HSCs as a targetable vulnerability by precise gene editing of SF3B1 K700E mutations in primary CD34+ cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

10 Samples

Download data: CSV

(Submitter supplied) The central nervous system (CNS) is surrounded by three membranes called meninges. Specialized fibroblasts, originating from the mesoderm and neural crest, primarily populate the meninges and serve as a binding agent. Our goal was to compare fibroblasts from meninges and skin obtained from the same human-aged donors, exploring their molecular and cellular characteristics related to CNS functions. We isolated meningeal fibroblasts (MFs) and skin fibroblasts (SFs) from brain donors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

15 Samples

Download data: TXT

(Submitter supplied) Joubert syndrome (JS) is a recessively inherited congenital ataxia characterized by hypotonia, psychomotor delay, abnormal ocular movements, intellectual disability and a peculiar cerebellar and brainstem malformation, the ’molar tooth sign’. Over 40 causative genes have been reported, all encoding for proteins implicated in the structure or functioning of the primary cilium, a subcellular organelle widely present in embryonic and adult tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

36 Samples

Download data: CSV

(Submitter supplied) Antisense oligonucleotide (ASO) nusinersen (Spinraza®) modulates the pre–mRNA splicing of the SMN2 gene, allowing rebalance of biologically active SMN. It is administered intrathecally via lumbar puncture after removing an equal amount of cerebrospinal fluid (CSF). Its effect was proven beneficial and approved since 2017 for SMA treatment. Since the direct effect of nusinersen on RNA metabolism, the aim of this project was to evaluate cell-free RNA (cfRNA) in CSF of SMA patients under ASOs treatment for biomarker discovery.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

36 Samples

Download data: DAT

(Submitter supplied) Aicardi-Goutières Syndrome (AGS) is a rare neuro-inflammatory disease characterized by increased expression of interferon-stimulated genes (ISGs). Disease-causing mutations are present in genes associated with innate antiviral responses. Disease presentation and severity vary, even between patients with identical mutations from the same family. This study investigated DNA methylation signatures in PBMCs to understand phenotypic heterogeneity in AGS patients with mutations in RNASEH2B. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL21145

17 Samples

Download data: IDAT, TXT

(Submitter supplied) Bisdemethoxycurcumin (BDC) might be inflammation inhibitor in AD. BDC is almost insoluble in water, poorly absorbed by the organism, and rapidly degraded. We developed a nanoformulation of BDC based on H-Ferritin nanocages (HFn).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

23 Samples

Download data: RESULTS

(Submitter supplied) Alzheimer’s disease (AD) and Lewy body dementia (LBD) are two different forms of dementia but their pathology may involve the same cortical areas with overlapping cognitive manifestation. Dementia cases within the same family share a common genetic background. Nonetheless, the clinical phenotype may be different due to the different underlying molecular processes that come-up apart from genetics, causing diverse neurodegeneration. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

48 Samples

Download data: RESULTS

(Submitter supplied) Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease caused by loss of motor neurons. SOD1 may have a toxic role in the pathogenesis of ALS when the protein aggregates in the cytoplasm; increased accumulation of soluble nuclear SOD1 (nSOD1) represents a protective cellular reaction.

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

30 Samples

Download data: RESULTS

(Submitter supplied) Investigating MINCR potential mechanisms of action and its implications in cancer and neurodegeneration in relation to its expression levels in SH-SY5Y cells through RNA-seq approach.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: RESULTS

(Submitter supplied) The DNA damage response (DDR) is the signaling cascade that recognizes DNA double-strand breaks (DSB) and promotes their resolution via the DNA repair pathways of Non-Homologous End Joining (NHEJ) or Homologous Recombination (HR). We and others have shown that DDR activation requires DROSHA. However, whether DROSHA exerts its functions by associating with damage sites, what controls its recruitment and how DROSHA influences DNA repair, remains poorly understood. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: BW

(Submitter supplied) SARS-Cov-2 infection is frequently associated with Nervous System (NS) manifestations. However, it is not clear how SARS-CoV-2 can cause neurological dysfunctions and which molecular processes affects. In this work, we examined the frontal cortex tissue of patients who died of COVID-19 for the presence of SARS-CoV-2, comparing qRT-PCR with ddPCR. We also investigated the transcriptomic profile of frontal cortex from COVID-19 patients and matched controls by RNA-seq analysis to characterize the transcriptional signature.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) Alzheimer’s disease (AD), Parkinson’s disease (PD) and Amyotrophic Lateral Sclerosis (ALS) are neurodegenerative disorders characterized by progressive degeneration of central or peripheral nervous system. A central role of RNA metabolism has emerged in these diseases, concerning mRNAs processing and non-coding RNAs biogenesis. We aimed to identify possible crossroads or deviations in the dysregulated pathways of AD, PD and ALS. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

23 Samples

Download data: TXT

(Submitter supplied) 3D cell cultures are becoming more and more important in the field of regenerative medicine due to their ability to mimic the cellular physiological microenvironment. Among the different types of 3D scaffolds, we focus on the Nichoid, a miniaturized scaffold with a structure inspired by the natural staminal niche. The Nichoid can activate cellular responses simply by subjecting the cells to mechanical stimuli. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: TXT

(Submitter supplied) 3D cell cultures are becoming more and more important in the field of regenerative medicine due to their ability to mimic the cellular physiological microenvironment. Among the different types of 3D scaffolds there is the Nichoid: an engineered 3D micro-scaffold with a structure inspired by the natural staminal niche. The Nichoid can activate cellular response simply by subjecting the cells to mechanical stimuli. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) We detected different deregulated RNAs in LEVs and SEVs from patients with Alzheimer's, Parkinson's Disease, Amyotrophic Lateral Sclerosis, ALS. MiRNAs resulted to be the most interesting subpopulation of transcripts transported by plasma derived SEVs since they appeared to discriminate all NDs disease from CTRLs and they can provide a signature for each NDs. Common enriched pathways for SEVs were mainly linked to ubiquitin mediated proteolysis and Toll-like receptor signaling pathways and for LEVs to neurotrophin signaling and Glycosphingolipid biosynthesis pathway.

Organism:

Homo sapiens

Type:

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

Platform:

GPL18573

144 Samples

Download data: TXT

(Submitter supplied) Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is associated with the most common type of dementia and is characterized by the presence of deposits of the protein fragment beta‐amyloid (Aβ) in the brain. The natural product mixture of curcuminoids that improves certain defects in innate immune cells of AD patients may selectively enhance Aβ phagocytosis by alteration of gene transcription. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15520

69 Samples

Download data: TSV

(Submitter supplied) Yeast Sen1Senataxin is a RNA/DNA helicase that preserves replication forks across RNA Polymerase II-transcribed genes by counteracting RNA:DNA hybrids accumulation. We show that in Sen1-depleted cells early forks clashing head-on with transcription halt, and impair progression of sister forks within the same replicon. Unsolved replication-transcription collisions trigger the local firing of dormant origins that rescue arrested forks. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

6 Samples

Download data: BEDGRAPH, CEL