Gene Expression Analysis of Laser Captired Purkinje Cells from the Post-Mortem Essential Tremor Cerebellum
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE197345 | GEO | 2023/02/28
REPOSITORIES: GEO
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Project description:Previous studies in bulk tissue suggest that there are abundant expression quantitative trait loci (eQTLs) in human brain. This sample series is of cerebellar Purkinje cells isolated using laser capture microdissection from human cases without neurological disease but of known genotypes. These data may be helpful in confirming eQTLs in bulk tissue or in mapping other gene expression traits in an enriched neuronal population. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249 The aim of this study was to examine gene expression in isolated purkinje cells from the human cerebellum. We obtained frozen brain tissue from the cerebellum. We stained sections with cresyl violet and separated Purkinje cells based on morphology and location within the cerebellum using laser capture microdissection. Expression analyses were then performed.
2013-01-01 | E-GEOD-37205 | biostudies-arrayexpress
Project description:We performed gene-expression analysis of mouse Purkinje cells as a model M-bM-^@M-^\single-type neuronM-bM-^@M-^]. DNA microarray analysis detected at least 7,055 genes in Purkinje cells, most of which are classified into functional molecule categories. Our comparative analysis between Purkinje cells and the granule cell layer showed that the characteristic expression pattern in Purkinje cells was particularly represented by M-bM-^@M-^\the neural communication systemM-bM-^@M-^] components. Pukinje cells and granule cell layer of the mouse cerebellum were collected by laser microdissection for RNA extraction and hybridization on Affymetrix microarrays.
2013-01-17 | E-GEOD-26749 | biostudies-arrayexpress
Project description:Previous studies in bulk tissue suggest that there are abundant expression quantitative trait loci (eQTLs) in human brain. This sample series is of cerebellar Purkinje cells isolated using laser capture microdissection from human cases without neurological disease but of known genotypes. These data may be helpful in confirming eQTLs in bulk tissue or in mapping other gene expression traits in an enriched neuronal population. Authorized Access data: Mapping of GEO sample accessions to dbGaP subject/sample IDs is available through dbGaP Authorized Access, see http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000249
2013-01-01 | GSE37205 | GEO
Project description:At present, the underlying neuronal mechanisms leading to an autism spectrum disorder (ASD) diagnosis have not been identified. However, studies from human postmortem ASD brains have consistently revealed disruptions in cerebellar circuitry, specifically with a reduction in Purkinje cell (PC) number and size. Alterations in cerebellar circuitry would have important implications for information processing within the cerebellum and affect a wide range of human motor and non-motor behaviors. Laser capture microdissection was performed to obtain pure PC populations from a cohort of postmortem control and ASD cases and transcriptional profiles were compared.
2022-10-01 | GSE211154 | GEO
Project description:We used laser capture microdissection to isolate both microvascular endothelial cells and neurons from post mortem brain tissue from patients with schizophrenia and bipolar disorder and healthy controls. RNA was isolated from these cell populations, amplified, and analysed using Affymetrix HG133plus2.0 GeneChips. In the first instance, we used the dataset to compare the neuronal and endothelial data, in order to demonstrate that the predicted differences between cell types could be detected using this methodology. Keywords: cell type comparison, laser capture microdissection
2008-12-18 | GSE12679 | GEO
Project description:Thiele2013 - Cerebellum Purkinje cells
The model of cerebellum Purkinje cells metabolism is derived from the community-driven global reconstruction of human metabolism (version 2.02, MODEL1109130000
).
This model is described in the article:
A community-driven global reconstruction of human metabolism.
Thiele I, et al
.
Nature Biotechnology
Abstract:
Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven,
consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared
with its predecessors, the reconstruction has improved topological and functional features, including ~2x more reactions and ~1.7x more unique metabolites. Using
Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic
data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically
generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will
facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.
This model is hosted on BioModels Database
and identified by: MODEL1310110050
.
To cite BioModels Database, please use: BioModels Database: An enhanced,
curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer
to CC0 Public Domain Dedication
for more information.
2005-01-01 | MODEL1310110050 | BioModels
Project description:Contactin-associated protein-like 2 (Caspr2) is a neurexin-like protein that has been associated with numerous neurological conditions. However, the mechanisms underlying Caspr2 function in the central nervous system remain incompletely understood. Here, we report on a functional role for Caspr2 in the developing cerebellum. Loss of Caspr2 impairs Purkinje cell dendritic development, alters cell signaling and results in motor coordination deficits. Caspr2 is highly enriched at synaptic specializations in the cerebellum. Using a proteomic approach, we identify type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) as a specific synaptic interaction partner of the Caspr2 extracellular domain (ECD) in the molecular layer (ML) of the developing cerebellum. The interaction of Caspr2 ECD with IP3R1 inhibits IP3R1-mediated changes in cellular morphology. Together, our work defines a mechanism by which Caspr2 controls the development and function of the cerebellum, and advances our understanding of how Caspr2 dysfunction might lead to specific brain disorders.
2020-07-13 | PXD018972 | Pride
Project description:We performed gene-expression analysis of mouse cerebellar granule cell layer as compared to that of Purkinje cells. DNA microarray analysis detected genes in cerebellar granule cell layer, most of which are classified into functional molecule categories. Our comparative analysis between Purkinje cells and the granule cell layer showed that the characteristic expression pattern in Purkinje cells was particularly represented by M-bM-^@M-^\the neural communication systemM-bM-^@M-^] components. Pukinje cells and granule cell layer of the mouse cerebellum were collected by laser microdissection for RNA extraction and hybridization on Affymetrix microarrays.
2013-01-17 | E-GEOD-26750 | biostudies-arrayexpress
Project description:Thirty-five adult (8-16 week old) C57BL/6 mice (which had undergone previous behavioral protocols) were anesthetized with isoflurane, and the brains were removed quickly, embedded in OCT, and frozen in a dry ice-ethanol mixture. The interval between decapitation and complete freezing was always less than 3 minutes. The brain was warmed up to -20oC, and cut into 10-14 m sections with a cryostat (Leica). Serial coronal sections were kept on slides in 100% ethanol until sectioning was complete. Tissue was then processed with hematoxylin and eosin (H&E) staining for cell layer visualization, followed by dehydration with increasing concentrations of ethanol and then xylene. We focused on two cell types, the Purkinje (Pk) and granule cells (gc) of the flocculus. We used an Arcturus PixCell II laser capture microdissection (LCM) scope to locate and capture cells from the appropriate areas, obtaining ten samples per cell type per mouse. We estimate that each Pk sample contained about 50-100 Purkinje cells, and each gc sample contained a few thousand granule cells. Granule cell samples (dorsal flocculus) were captured before Purkinje cell samples, to reduce contamination of the Purkinje cell samples by granule cell material. Samples were removed from the LCM caps with RNEasy lysis buffer (Qiagen) containing 1% -mercaptoethanol, then frozen at -80oC. For each mouse, all the samples of a given cell type were pooled together; samples from different mice were not pooled. Total RNA samples were isolated using RNEasy kits (Qiagen), then amplified in two rounds of in vitro transcription (IVT) using the Ambion MessageAmp aRNA kit. IVT-amplified samples were hybridized to microarrays if the end product after the second round of amplification was of concentration greater than or equal to 0.2 g/l, and at least 10 times the negative control signal (measured after two rounds of amplification of a blank sample). Due to the small starting sample sizes, samples often were rejected due to insufficient quantity for hybridization: thus, 18/35 granule cell samples and 23/35 Purkinje cell samples survived this quality control process, and were run on arrays (41 arrays total). Mus musculus spotted cDNA microarrays (MM arrays) containing ~42,000 spots were obtained from the Stanford Functional Genomics facility (complete information at http://www.microarray.org/), in order to analyze gene expression in each cell type. We used a type II experimental design, where all experimental samples were hybridized against a common reference sample for multi-way comparison. The reference sample comprised mRNA extracted from neonatal and adult brain and liver, and amplified twice by IVT. We used standard protocols for cDNA labeling, as well as array hybridization, washing, scanning, and data analysis (http://cmgm.stanford.edu/pbrown/protocols/index.html).
2006-10-09 | E-SMDB-3779 | biostudies-arrayexpress
Project description:Loss of Tmem106b leads to cerebellum Purkinje cell death and motor deficits
| PRJNA693266 | ENA