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1,315 results for “aberration”
Aberrant accumulation of Kras-dependent enhancer RNAs during tumor progression renders cancer cells susceptible to PAF1 depletion due to R-loop accumulation I
GEO Series GSE217740. Mus musculus. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Integration of genome-wide DNA methylation and transcription uncovered aberrant methylation-regulated genes and pathways in the peripheral blood mononuclear cells of systemic sclerosis
GEO Series GSE117931. Homo sapiens. 74 samples. Type: Expression profiling by array; Methylation profiling by array.
Aberrant super-enhancer landscape in enzalutamide-resistant prostate cancer cells
GEO Series GSE228308. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The spindle assembly checkpoint is a therapeutic vulnerability of CDK4/6 inhibitor-resistant ER+ breast cancer with mitotic aberrations
<p>This study aims to investigate the accumulation of genomic instability and chromosome segregation errors after the acquisition of resistance to CDK4/6i in ER+ breast cancer and to test the efficacy of mitotic kinase inhibitors as a potential treatment for CDK4/6i-resistant breast cancer patients.</p> <p><strong>This repository contains whole-exome and shallow whole-genome sequencing from luminal breast cancer patient-derived organoid (BPTO.95 #1 and #2) both at the untreated or Parental state and post resistance to Palbociclib</strong>.</p> <p>Palbociclib resistance was developed by continuous dose-escalation of palbociclib up to 0.5-1 μM until cell growth was observed in the presence of the drug (10-12 months for PDO). During this time, parental cell lines and organoids were cultured in regular media to match the time spent in culture. Once resistance was established, Palbo-R PDOs were cultured in a regular growth medium without palbociclib. Cells were cultured without palbociclib for at least two weeks before evaluating resistance.</p>
Dataset related to the article "Enduring Reactive Oxygen Species Emission Causes Aberrant Protein S-Glutathionylation Transitioning Human Aortic Valve Cells from a Sclerotic to a Stenotic Phenotype"
<p>This record contains raw data related to the article "Enduring Reactive Oxygen Species Emission Causes Aberrant Protein S-Glutathionylation Transitioning Human Aortic Valve Cells from a Sclerotic to a Stenotic Phenotype"</p> <p><strong><em>Aims:</em></strong> During calcific aortic valve stenosis (CAVS) progression, oxidative stress and endothelial dysfunction mark the initial pathogenic steps with a parallel dysregulation of the antioxidant systems. Here, we tested whether oxidation-induced protein S-glutathionylation (P-SSG) accounts for a phenotypic switch in human aortic valvular tissue, eventually leading to calcium deposition. Next, we tested whether countering this reactive oxygen species (ROS) surge would prevent these perturbations. <strong><em>Results:</em></strong> We employed state-of-the-art technologies, such as electron paramagnetic resonance (EPR), liquid chromatography-tandem mass spectrometry, imaging flow-cytometry, and live-cell imaging on human excised aortic valves and primary valve endothelial cells (VECs). We observed that a net rise in EPR-detected ROS emission marked the transition from fibrotic to calcific in human CAVS specimens, coupled to a progressive increment in P-SSG deposition. In human VECs (hVECs), treatment with 2-acetylamino-3-[4-(2-acetylamino-2-carboxyethylsulfanylthiocarbonylamino)phenylthiocarbamoylsulfanyl]propionic acid triggered highly oxidizing conditions prompting P-SSG accumulation, damaging mitochondria, and inducing endothelial nitric oxide synthase uncoupling. All the events conjured up in morphing these cells from their native endothelial phenotype into a damaged calcification-inducing one. As proof of principle, the use of the antioxidant N-acetyl-L-cysteine prevented these alterations. <strong><em>Innovation:</em></strong> Borne as a compensatory system to face excessive oxidative burden, with time, P-SSG contributes to the morphing of hVECs from their innate phenotype into a damaged one, paving the way to calcium deposition. <strong><em>Conclusion:</em></strong> Our data suggest that, in the human aortic valve, unremitted ROS emission along with a P-SSG build-up occurs and accounts, at least in part, for the morphological/functional changes leading to CAVS.</p>
Supplementary processed data for Chandler et al. Single-cell transcriptomics identifies aberrant glomerular angiogenic signalling in the early stages of a murine model of WT1 kidney disease
<p><strong><em>Summary datafiles for Chandler et al.</em></strong></p> <ul> <li>Processed single-cell RNA sequencing data, derived from murine glomeruli (isolated using the dynabead technique) from <em>n = 2</em> wild-type <em>Wt1<sup>+/+</sup></em> (Ctrl) and <em>n = 2</em> mutant <em>Wt1<sup>R394W/+</sup></em> (Mut) littermates of WT1 glomerulopathy, followed by 10x Genomics Chromium v3 platform.</li> <li>Please refer to associated scripts for analysis of the data: <a href="https://github.com/daniyal-jafree1995/collaborations/blob/main/Chandleretal_2022_WT1glomerulopathyscRNAseq.R">https://github.com/daniyal-jafree1995/collaborations/blob/main/Chandleretal_2022_WT1glomerulopathyscRNAseq.R</a> </li> <li>File descriptions as below: <ul> <li>barcodes.tsv.gz - barcodes file required for input to Read10X function in Seurat</li> <li>features.tsv.gz - features file required for input to Read10X function in Seurat</li> <li>matrix.mtx.gz - matrix file required for input to Read10X function in Seurat</li> <li>WT1_scRNAseq.rds - RDS file containing processed and annotated Seurat object for downstream analysis</li> </ul> </li> </ul>
Aberrantly expressed long noncoding RNAs in the eutopic endometrium of women with adenomyosis
GEO Series GSE68870. Homo sapiens. 8 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
chromosomal aberrations in prostate cancer
GEO Series GSE6040. Homo sapiens. 18 samples. Type: Genome variation profiling by array.
TCR and BCR loci copy number aberration detection for FFPE tissues using MIP-based assay
GEO Series GSE111052. Homo sapiens. 63 samples. Type: Genome variation profiling by SNP array.
Mild SARS-CoV-2 maternal infection in mice induces transient offspring neurodevelopmental aberrance
GEO Series GSE317803. Mus musculus. 140 samples. Type: Expression profiling by high throughput sequencing.
Aberrant gene expression leakage from linage-specific heterochromatic loci during senescence
GEO Series GSE180469. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Identification of novel sub-microscopic copy number aberrations in adult acute myeloid leukemia
GEO Series GSE20672. Homo sapiens. 112 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Loss of function mutation in progressive ankylosis (Ank) gene causes aberrant mineralization and acquisition of osteoblast-like-phenotype by annulus fibrosus cells in the intervertebral disc
GEO Series GSE206997. Mus musculus. 20 samples. Type: Expression profiling by array.
Data Set from Renna LV, Bosè F, Brigonzi E, Fossati B, Meola G, Cardani R. Aberrant insulin receptor expression is associated with insulin resistance and skeletal muscle atrophy in myotonic dystrophies. PLoS One. 2019 Mar 22;14(3):e0214254. doi: 10.1371/journal.pone.0214254. PMID: 30901379; PMCID: PMC6430513.
<p>Data Set from Renna LV, Bosè F, Brigonzi E, Fossati B, Meola G, Cardani R. Aberrant insulin receptor expression is associated with insulin resistance and skeletal muscle atrophy in myotonic dystrophies. PLoS One. 2019 Mar 22;14(3):e0214254. doi: 10.1371/journal.pone.0214254. PMID: 30901379; PMCID: PMC6430513.</p> <p> </p> <p>This is the abstact:</p> <p>Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are autosomal dominant multisystemic disorders linked to two different genetic loci and characterized by several features including myotonia, muscle atrophy and insulin resistance. The aberrant alternative splicing of insulin receptor (IR) gene and post-receptor signalling abnormalities have been associated with insulin resistance, however the precise molecular defects that cause metabolic dysfunctions are still unknown. Thus, the aims of this study were to investigate in DM skeletal muscle biopsies if beyond INSR missplicing, altered IR protein expression could play a role in insulin resistance and to verify if the lack of insulin pathway activation could contribute to skeletal muscle wasting. Our analysis showed that DM skeletal muscle exhibits a lower expression of the insulin receptor in type 1 fibers which can contribute to the defective activation of the insulin pathway. Moreover, the aberrant insulin signalling activation leads to a lower activation of mTOR and to an increase in MuRF1 and Atrogin-1/MAFbx expression, possible explaining DM skeletal muscle fiber atrophy. Taken together our data indicate that the defective insulin signalling activation can contribute to skeletal muscle features in DM patients and are probably linked to an aberrant specific-fiber type expression of the insulin receptor.</p>
Single cell spatial temporal atlas of murine skeletal muscle undergoing normal regeneration, aberrant repair, and aging
<p>CODEX images and single cell data set of murine skeletal muscle undergoing normal regeneration, aberrant repair, and in aging. Accompanying the manuscript, Wang et al. "<strong>A single cell spatial temporal atlas of skeletal muscle reveals cellular neighborhoods that orchestrate regeneration and become disrupted in aging</strong>".</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.