Ontology highlight
ABSTRACT:
PROVIDER: PRJNA544731 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-seq of human monocytes from subjects affected with multiple sclerosis
2019-05-14 | E-GEOD-77598 | ExpressionAtlas
Project description:<p>Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. In this study, we applied single nucleus RNA sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types, many of which are relatively sparse. Additionally, we found that excitatory types are less layer-restricted than expected based prior knowledge from cell morphologies and from mouse studies. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous cell types in human and mouse, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.</p> <p>This study conducted by the Allen Institute for Brain Science was supported by the Allen Institute for Brain Science and by US National Institutes of Health grant U01 MH114812-02 to E.S.L. Collaborators request that publications resulting from these data cite their original publication: Hodge RD, Bakken TE, et al. Conserved cell types with divergent features between human and mouse cortex. bioRxiv. 2018 doi: <a href="https://www.biorxiv.org/content/10.1101/384826v1" target="_blank">10.1101/384826</a>.</p>
| phs001790 | dbGaP
Project description:Using the Illumina 450K array and a stringent statistical analysis with age and gender correction, we report genome-wide differences in DNA methylation between pathology-free regions derived from human multiple sclerosis–affected and control brains. Differences were subtle, but widespread and reproducible in an independent validation cohort. The transcriptional consequences of differential DNA methylation were further defined by genome-wide RNA-sequencing analysis and validated in two independent cohorts. Genes regulating oligodendrocyte survival, such as BCL2L2 and NDRG1, were hypermethylated and expressed at lower levels in multiple sclerosis–affected brains than in controls, while genes related to proteolytic processing (for example, LGMN, CTSZ) were hypomethylated and expressed at higher levels. These results were not due to differences in cellular composition between multiple sclerosis and controls. Thus, epigenomic changes in genes affecting oligodendrocyte susceptibility to damage are detected in pathology-free areas of multiple sclerosis–affected brains.
2013-11-24 | GSE40360 | GEO
Project description:To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects.
| EGAD00001006575 | EGA
Project description:Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues.
2017-12-11 | GSE97887 | GEO
Project description:We performed single-nucleus RNA-sequencing of the cortex of APOE3 and APOE4 knock-in (KI)flox/flox mice to investigate the effects of human APOE4 gene on cell-specific signaling mechanisms at the BBB and in the brain.
2022-08-22 | GSE185063 | GEO
Project description:In the present study we addressed several questions related to the mechanisms of cortical injury. We analyzed genome wide gene expression by microarrays, comparing active multiple sclerosis lesions with highly inflammatory lesions of chronic tuberculous meningitis, with neurodegenerative lesions of Alzheimer’s disease and with normal cortex of age matched controls. To clarify which inflammatory mediators drive demyelination in the human cortex, we characterized and compared the gene expression profile of cortices derived from patients with progressive Multiple Sclerosis (pMS), Meningitis tuberculosis (MT), Alzheimers disease (AD) as well as of normal cortex from age matched controls. 3 cases of each disease were included into the study. Preceding the gene expression profiling all cases were characterized histologically and areas of interest were identified. RNA was isolated from those areas, amplified and hybridized to Agilent G4112F whole genome microarrays.
2011-10-05 | E-GEOD-32645 | biostudies-arrayexpress
Project description:Basal radial glial cells (bRGs) are neural progenitors enriched in primates and humans and were proposed to contribute to the expansion of neurons during cortical development in gyrencephalic species. Shortly after their generation, bRGs delaminate towards the outer subventricular zone, where they divide multiple times before differentiation. Thus, the regulation of bRGs generation could be essential for the establishment of correct gyrification within the human cortex. Here, we study the role of LGALS3BP, a secreted protein whose RNA expression is enriched in bRGs. By using cerebral organoids, human fetal tissues and mice, we show that manipulation of LGALS3BP regulated bRG generation. Additionally, individuals with unique de novo variants in LGALS3BP demonstrate abnormal gyrification and thickness at multiple sites over their cortex. Single-cell-RNA-sequencing and proteomics reveal the extracellular matrix involvement in the LGALS3BP mediated mechanisms. We find that LGALS3BP is required for bRGs delamination and influences corticogenesis and gyrification in humans.
2021-10-26 | PXD015878 | Pride