Ontology highlight
ABSTRACT:
PROVIDER: PRJNA786429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17138738_1.fastq.gz | Fastqsanger.gz | |||
| SRR17138738_2.fastq.gz | Fastqsanger.gz | |||
| SRR17138739_1.fastq.gz | Fastqsanger.gz | |||
| SRR17138739_2.fastq.gz | Fastqsanger.gz | |||
| SRR17138740_1.fastq.gz | Fastqsanger.gz |
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Project description:Single cell transcriptomic and chromatin profiles suggest Layer Vb is the only layer with shared excitatory cell types in the medial and lateral entorhinal cortex.
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Project description:We report the first full transcriptome analysis of layer II and deep layers of the medial and lateral entorhinal cortex during postnatal development. Our analysis showed that postnatal timepoint was the most important element in entorhinal cortex transcriptional dynamics, followed by laminar differences. There were fewer differentially expressed genes between the medial and lateral parts of the entorhinal cortex, and most of these were found in layer II.
2017-08-01 | GSE85789 | GEO
Project description:All brain functionality arises from the activity in neural circuits in different anatomical regions. These regions contain different circuits comprising unique cell types. An integral part to understanding neural circuits is a full census of the constituent parts, i.e., the neural cell types. This census can be based on different characteristics. Previously combinations of morphology and physiology, gene expression, and chromatin accessibility have been used in various cortical and subcortical regions. This has given an extensive yet incomplete overview of neural cell types. However, these techniques have not been applied to all brain regions. Here we apply single cell analysis of accessible chromatin on two similar but different cortical regions, the medial and the lateral entorhinal cortices. Even though these two regions are anatomically similar, their intrinsic and extrinsic connectivity are different. In 4136 cells we identify 20 different clusters representing different cell types. As expected, excitatory cells show regionally specific clusters, whereas inhibitory neurons are shared between regions. We find that several deep layer excitatory neuronal cell types as defined by chromatin profile are also shared between the two different regions. Integration with a larger scRNA-seq dataset maintains this shared characteristic for cells in Layer Vb. Interestingly, this Layer contains three clusters, two specific to either subregion and one shared between the two. These clusters can be putatively associated with particular functional and anatomical cell types found in this layer. This information is a step forwards into elucidating the cell types within the entorhinal circuit and by extension its functional underpinnings.
2021-12-28 | GSE192567 | GEO
Project description:The perforant path provides the main cortical excitatory input to the hippocampus. Due to its important role in information processing and coding, entorhinal projections to the dentate gyrus have been studied in considerable detail. Nevertheless, a characterization of synaptic transmission between individual connected pairs of entorhinal stellate cells and dentate granule cells is still pending. Here, we have used organotypic entorhino-hippocampal tissue cultures, in which the entorhino-dentate (EC-GC) projection is present and EC-GC pairs can be studied using whole-cell patch clamp recordings. Using cultures of wildtype mice, the properties of EC-GC synapses formed by afferents from the lateral and medial entorhinal cortex were compared and differences in short-term plasticity were revealed. Since the perforant path is severely affected in Alzheimer´s disease, we used cultures of APP-deficient mice to address the role of the amyloid-precursor protein (APP) at this synapse. APP-deficiency caused alterations in excitatory neurotransmission at medial perforant path synapses that were accompanied by transcriptomic and ultrastructural changes. Moreover, the deletion of pre- but not postsynaptic APP through the local injection of Cre-expressing AAVs in conditional APPflox/flox tissue cultures increased the efficacy of neurotransmission at perforant path synapses. Together, these data suggest a physiological role for presynaptic APP at medial perforant path synapses, which may be adversely affected under conditions of altered APP processing.
2022-09-16 | GSE213284 | GEO
Project description:Understanding the mechanisms by which long-term memories are formed and stored in the brain represents a central aim of neuroscience. Prevailing theory suggests that long-term memory encoding involves early plasticity within hippocampal circuits, while reorganization of the neocortex is thought to occur weeks to months later to subserve remote memory storage. Here we report that long-term memory encoding can elicit early transcriptional, structural and functional remodeling of the neocortex. Parallel studies using genome-wide RNA-sequencing, ultrastructural imaging, and whole-cell recording in wild-type mice suggest that contextual fear conditioning initiates a transcriptional program in the medial prefrontal cortex (mPFC) that is accompanied by rapid expansion of the synaptic active zone and postsynaptic density, enhanced dendritic spine plasticity, and increased synaptic efficacy. To address the real-time contribution of the mPFC to long-term memory encoding, we performed temporally precise optogenetic inhibition of excitatory mPFC neurons during contextual fear conditioning. Using this approach, we found that real-time inhibition of the mPFC inhibited activation of the entorhinal-hippocampal circuit and impaired the formation of long-term associative memory. These findings suggest that encoding of long-term episodic memory is associated with early remodeling of neocortical circuits, identify the prefrontal cortex as a critical regulator of encoding-induced hippocampal activation and long-term memory formation, and have important implications for understanding memory processing in healthy and diseased brain states. 4 biological replicates per group were analyzed. The material analyzed was medial prefrontal cortex (mPFC; anterior cingulate cortex subregion) from both brain hemispheres, from which total RNA was extracted.
2014-06-16 | E-GEOD-58510 | biostudies-arrayexpress
Project description:The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions; the medial, dorsal, lateral, rostral, and occipital, from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array. Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital
2007-12-13 | E-GEOD-929 | biostudies-arrayexpress
Project description:Sanfilippo syndrome type B (MPS III B) is an autosomal recessive, neurodegenerative disease of children, characterized by profound mental retardation and dementia. The primary cause is mutation in the NAGLU gene, resulting in deficiency of N-acetylglucosaminidase and lysosomal accumulation of heparan sulfate. In the mouse model of MPS III B, neurons and microglia display the characteristic vacuolation of lysosomal storage of undegraded substrate, but neurons in the medial entorhinal cortex (MEC) display accumulation of several additional substances. We used whole genome microarray analysis to examine differential gene expression in MEC neurons isolated by laser capture microdissection from Naglu -/- and Naglu +/- mice. Neurons from the lateral entorhinal cortex (LEC) were used as tissue controls. The highest increase in gene expression (6- to 7-fold between mutant and control) in MEC and LEC neurons was that of Lyzs, which encodes lysozyme, but accumulation of lysozyme protein was seen in MEC neurons only. Because of a report that lysozyme induced the formation of hyperphosphorylated tau (P-tau) in cultured neurons, we searched for P-tau by immunohistochemistry. P-tau was found in MEC of Naglu -/- mice, in the same neurons as lysozyme. In older mutant mice, it was also seen in the dentate gyrus, an area important for memory. Electron microscopy of dentate gyrus neurons showed cytoplasmic inclusions of paired helical filaments - P-tau aggregates characteristic of tauopathies, a group of age-related dementias that includes Alzheimer disease. Our findings indicate that the Sanfilippo syndrome type B should also be considered a tauopathy. Two-condition experiment, Naglu-/- (affected) vs. Naglu+/- (unaffected control) of neurons from two adjacent brain regions: medial entorhinal cortex (MEC) and lateral entorhinal cortex (LEC). Biological replicates: 3 MEC Naglu-/-, 3 MEC Naglu+/-, 3 LEC Naglu-/- and 3 LEC Naglu+/-. Comparisons were made between 3 pairs of mutant and control female littermates for MEC and LEC neurons with dye switch duplicates, for a total of 12 microarrays.
2009-04-22 | E-GEOD-15758 | biostudies-arrayexpress
Project description:To examine how miRNAs differ between medial entorhinal cortex layers during postnatal development, we analyzed the miRNA expression in layer II and the deep layers (III-VI) at postnatal ages P2, P9, P23 and P45 in wildtype Long Evans rats. The expression of the two most significantly differentially expressed miRNAs were validated by in situ hybridization.
2017-08-01 | GSE85753 | GEO
Project description:The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions; the medial, dorsal, lateral, rostral, and occipital, from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array. Keywords = mouse Keywords = cortex Keywords = development Keywords = regional Keywords = gene expression Keywords = medial Keywords = dorsal Keywords = lateral Keywords = rostral Keywords = occipital Keywords: ordered
2004-03-27 | GSE929 | GEO
Project description:Alzheimer’s disease (AD) is the most common neurodegenerative disorder being characterized by progressive impairment of memory and cognition, resulting in dementia. To investigate brain region vulnerability to AD and which pathways are altered in certain areas in AD, we performed proteomic profiling of human brain samples during AD progression in regions early (medial temporal lobe - MTL) and late affected (neocortex) by tau pathology. We employed a mass spectrometry-based approach to interrogate the human brain proteome during AD progression (B/B stages) in four distinct brain regions: entorhinal cortex (EC), parahippocampal cortex (PHC), temporal cortex (TC) and frontal cortex (FC). Importantly, we wanted to evaluate brain areas that are affected by tau pathology in different disease stages, in order to gain insights if there are common mechanisms or patterns shared between different brain regions during disease progression. A total of 103 samples were analyzed by nanoLC-MS/MS.
2019-07-01 | PXD010138 | Pride