Ontology highlight
ABSTRACT:
PROVIDER: PRJNA612974 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Neural circuits in the medial entorhinal cortex (MEC) encode an animal’s position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH) images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.
2014-12-01 | GSE63300 | GEO
Project description:MEC AD different control genome sequencing Raw sequence reads
| PRJNA482727 | ENA
Project description:MEC-AD-cathode-size genome sequencing Raw sequence reads
| PRJNA482725 | ENA
Project description:Several methicillin resistance (SCCmec) clusters characteristic of hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) strains harbor the psm-mec locus. In addition to encoding the cytolysin, phenol-soluble modulin (PSM) mec, this locus has been attributed gene regulatory functions. Here we employed genome-wide transcriptional profiling to define the regulatory function of the psm-mec locus. The immune evasion factor protein A emerged as the primary conserved and strongly regulated target of psm-mec, an effect we show is mediated by the psm-mec RNA. Furthermore, the psm-mec locus exerted regulatory effects that were more moderate in extent and possibly mediated by the PSM-mec peptide. For example, expression of PSM-mec limited expression of mecA, thereby decreasing methicillin resistance. Our study shows that the psm-mec locus has a rare dual regulatory RNA and encoded cytolysin function, both with the potential to enhance MRSA virulence. Furthermore, our findings reveal a specific mechanism underscoring the recently emerging concept that S. aureus strains balance pronounced virulence and high expression of antibiotic resistance.
2017-08-29 | GSE51366 | GEO
Project description:Functional analysis of psm-mec RNA in staphylococcal species
| PRJDB5480 | ENA
Project description:Lipid droplets are secreted into milk by a complex process which begins by burgeoning oflipids at the endoplasmic reticulum of the mammary epithelial cell (MEC). Lipid dropletsenveloped by organelle-derived phospholipids reach the apical pole of the cell where they arewrapped by the plasma membrane to be secreted as fat globules into milk. Analyzing the fineprotein composition of the Milk Fat Globule Membrane (MFGM), the triple-layeredmembrane surrounding milk lipid droplets can therefore provide mechanistic clues to betterunderstand lipid droplet biosynthesis and secretion pathways. We combined a high sensitiveQ Exactive LC-MS/MS analysis of MFGM-derived peptides with the use of an in-house database intended to improve protein identification in the goat species. Using this approach, we performed the identification of 442 functional groups of proteins in the MFGM from goatmilk. To get a more comprehensive view of intracellular mechanisms driving lipid dropletdynamics in the MEC, we decided to investigate for the first time whether MFGM proteinswere phosphorylated. A phosphopeptide enrichment approach let us pinpoint 271 sites ofphosphorylation on 124 unique goat MFGM proteins. Enriched gene ontology termsassociated with phosphorylated MFGM proteins were protein transport and actin cytoskeletonorganization. Gained data are discussed with regard to lipid secretory mechanisms in the MEC.
2015-05-12 | PXD001039 | Pride