Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single Nucleus Transcriptomes from the Ventral Midbrain of Opioid Overdose Cases and Controls

ABSTRACT: Single Nucleus Transcriptomes from the Ventral Midbrain of Opioid Overdose Cases and Controls

PROVIDER: PRJNA1003845 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Single Nucleus Transcriptomes from the Ventral Midbrain of Opioid Overdose Cases and Controls

Project description:Dynamic interactions of neurons and glia in the ventral midbrain (VM) mediate reward and addiction behavior. We studied gene expression in 212,713 VM single nuclei from 95 human opioid overdose cases and drug-free controls. Chronic exposure to opioids left numerical proportions of VM glial and neuronal subtypes unaltered, while broadly affecting glial transcriptomes, involving 9.5 - 6.2% of expressed genes within microglia, oligodendrocytes, and astrocytes, with prominent activation of the immune response including interferon, NFkB signaling, and cell motility pathways, sharply contrasting with down-regulated expression of synaptic signaling and plasticity genes in VM non-dopaminergic neurons. VM transcriptomic reprogramming in the context of opioid exposure and overdose included 325 genes with genetic variation linked to substance use traits in the broader population, thereby pointing to heritable risk architectures in the genomic organization of the brain’s reward circuitry.

2023-08-18 | GSE240457 | GEO

'Single nucleus transcriptomes from the ventral midbrain of opioid overdose cases and controls'

Project description:'Single nucleus transcriptomes from the ventral midbrain of opioid overdose cases and controls'

| PRJNA954963 | ENA

'Single nucleus transcriptomes from the ventral midbrain of opioid overdose cases and controls'

Project description:'Single nucleus transcriptomes from the ventral midbrain of opioid overdose cases and controls'

| PRJNA954962 | ENA

Molecular diversity and migration of GABAergic neurons in the developing ventral midbrain

Project description:single-cell RNA sequencing data (plate-based CelSeq2) of developing mouse ventral midbrain GABAergic neurons. vmbGABA series contains E16 and P0 VGAT mouse ventral midbrain and E16 and P0 VGAT/PITX3 co-expressing mouse ventral midbrain.

2024-10-08 | GSE268378 | GEO

Chronic opioid treatment arrests neurodevelopment and alters synaptic activity in human midbrain organoids

Project description:Understanding the impact of long-term opioid exposure on the embryonic brain is critical due to the surging number of pregnant mothers with opioid dependency, but has been limited by human brain inaccessibility and cross-species differences in animal models. Here we establish a human midbrain model that uses hiPSC-derived midbrain organoids and apply it to assess cell-type-specific responses to acute and chronic fentanyl treatment and fentanyl withdrawal. Single-cell mRNA sequencing of 25,510 cells from organoids in different treatment groups indicated that chronic fentanyl treatment arrests neuronal subtype specification during early midbrain development and alters synaptic activity and neuron projection. In contrast, acute fentanyl treatment increases dopamine release but does not significantly alter gene expression related to cell lineage development. These results provide the first examination of the effects of opioid exposure on human midbrain development at the single cell level.

2024-03-05 | GSE260711 | GEO

Expression data from mouse ventral midbrain

2014-02-19 | GSE55119 | GEO

Differential expression between floor plate and ventral lateral region in E10.5 mouse embryo midbrain

Project description:The data revealed differential expression between floor plate and ventral lateral region in E10.5 mouse embryo midbrain. Several differentially expressed genes in these regions have been reported in the literature, demonstrating reliability of tissue dissection. Midbrain floor plate and non-overlapping adjacent ventral lateral region of mouse E10.5 embryo midbrain was dissected. Each sample was a pool from 6 embryos. Three replicates for each region were used for the experiment.

2011-05-18 | E-GEOD-25178 | biostudies-arrayexpress

Expression data from mouse ventral midbrain

Project description:The circadian nature of mood and its dysfunction in affective disorders is well recognized, but the underlying molecular mechanisms are still unclear. We showed that the circadian nuclear receptor REV-ERBa, which is associated with bipolar disorder, impacts midbrain dopamine production and mood-related behavior in mice. Genetic deletion of the Rev-erba gene or pharmacological inhibition of REV-ERBa activity in the ventral midbrain induced mania-like behavior in association with a central hyperdopaminergic state. We used microarrays to identify differentially expressed genes in the ventral midbrains of wild-type (WT) and Rev-erba knock-out (RKO) mice. Male RKO and WT mice (10-15 weeks of age) were maintained in a C57BL/6J background. Mice were housed in temperature-controlled (22-23ÂºC) quarters under a 12-h light-dark (LD) photoperiod (lights on at 8:00 a.m.). After entrainment for >10 days under LD conditions, mice were kept in constant darkness (DD) for 2 days starting at lights-off time. On the third day, mice were sacrificed at indicated time points by cervical dislocation.

2014-02-19 | E-GEOD-55119 | biostudies-arrayexpress

Identifying secreted biomarkers of dopaminergic ventral midbrain progenitor cells

Project description:Ventral midbrain (VM) dopaminergic progenitor cells derived from human pluripotent stem cells have the potential to replace endogenously lost dopamine neurons and are currently in preclinical and clinical development for treatment of Parkinson’s Disease (PD). However, one main challenge in the quality control of the cells is that rostral and caudal VM progenitors are extremely similar transcriptionally though only the caudal VM cells give rise to dopaminergic neurons with functionality in PD. Therefore, it is critical to develop assays which can rapidly and reliably discriminate rostral from caudal VM cells during clinical manufacturing. Here, we applied shotgun proteomics to search for novel secreted biomarkers specific for caudal VM progenitors compared to rostral VM progenitors and validated key hits by ELISA. From this, we identified novel secreted markers (CPE, LGI1 and PDGFC) significantly enriched in caudal versus rostral VM progenitor cultures, whereas the markers CNTN2 and CORIN were significantly enriched in rostral VM cultures. With this data, we suggest and test in clinical grade samples a panel of coupled ELISA assays that can be applied as a quality control tool for assessing the correct patterning of cells during clinical manufacturing.

2023-12-13 | PXD039510 | Pride

Repeated cocaine or methamphetamine treatment alters astrocytic CRF2 and GLAST expression in the ventral midbrain: RNA sequencing data

Project description:We describe the effects of cocaine and methamphetamine treatment on astrocytic expression of the corticotropin releasing factor 2 receptor and the excitatory amino acid transporter 1 in the ventral midbrain. The RNA-sequencing data confirms the expression of CRF2R on astrocytes using the Aldh1l1-NuTRAP model. This allowed for astrocyte mRNA isolation and characterization, confirming CRF2R expression on ventral midbrain astrocytes.

2021-10-15 | GSE184497 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data