Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The single cell transcriptomic profiling in iPSC derived Midbrain Organoid of POLG Disease

ABSTRACT: The single cell transcriptomic profiling in iPSC derived Midbrain Organoid of POLG Disease

PROVIDER: PRJNA1009590 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

The single cell transcriptomic profiling in iPSC derived Midbrain Organoid of POLG Disease

Project description:To investigate the transcriptomic profile and molecular mechanisms using single cell RNA sequecning (scRNA-seq) analysis for the iPSC derived midbrain organoids from the patient of POLG Disease

2023-09-28 | GSE241743 | GEO

RNA-seq of human midbrain organoid models of Parkinson's Disease

Project description:Parkinson’s disease (PD) is a prevalent neurodegenerative disorder that is characterized by the selective loss of midbrain dopamine (DA)-producing neurons and the formation of α-synuclein (α-syn)-containing inclusions named Lewy bodies (LBs). Here, we report that the loss of glucocerebrosidase (GCase), coupled with α-syn overexpression, result in substantial accumulation of detergent-resistant α-syn aggregates and Lewy body-like inclusions (LBLIs) in human midbrain-like organoids (hMLOs). These LBLIs exhibit a highly similar structure to PD-associated LBs, by displaying a spherically symmetric morphology with an eosinophilic core, and containing α-syn and ubiquitin. Importantly, hMLOs generated from PD patient-derived inducible pluripotent stem cells (iPSCs) harboring SNCA triplication also exhibit subsequent degeneration of DA neurons and LBLI formation upon chronic GCase inhibitor treatment. Taken together, our hMLOs harbouring two major PD risk factors (GCase deficiency and overproduced α-syn) successfully recapitulate major pathophysiological signatures of the disease, and highlight the broad utility of brain organoid technology in modeling human neurodegenerative diseases.

2021-08-13 | E-MTAB-7302 | biostudies-arrayexpress

RNA sequencing in POLG-iPSC derived brain cells

Project description:RNA sequencing in POLG-iPSC derived brain cells

| PRJNA853311 | ENA

Bulk RNA-seq of MilliporeSigma 3DGro human patient-derived gastrointestinal organoid lines compared to SCC300 human iPSC-derived colon organoid line

Project description:Transcriptomic profiles of 6 commercially-available human patient-derived gastrointestinal organoid lines were obtained and compared to transcriptomic profile of a commercially available human iPSC-induced colon organoid line. Transcriptomic profile of iPSC-derived human colon organoid line was compared after culture in either Corning growth-factor-reduced Matrigel (Corning 356231) or MilliporeSigma growth-factor-reduced ECMGel (E6909)

2022-03-31 | E-MTAB-11557 | biostudies-arrayexpress

snRNA-Seq data of human iPSC-midbrain organoids without and with microglia

Project description:The human brain is a complex, three-dimensional structure. To better recapitulate the brain complexity, recent efforts focused on the development of human specific midbrain organoids. Midbrain organoids consist of differentiated and functional neurons, which contain active synapses, as well as astroglia and oligodendrocytes. However, the absence of microglia, with their ability to phagocyte apoptotic cells and debris represents a major disadvantage for the midbrain organoid system. Additionally, neuro-inflammation-related disease modeling is not possible in the absence of microglia. So far, no studies about the effects of iPSC-derived microglia in brain organoid neural cells have been published. Here we describe an approach to derive microglia from human iPSCs and integrate them into midbrain organoids. Using single nuclear RNA sequencing in collaboration with the RIKEN institute we provide a detailed characterization of the microglia in brain organoids as well as of the influence their presence has on the other cells of the organoids.

2022-09-18 | GSE213288 | GEO

Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (passages)

Project description:Midbrain organoids are advanced in vitro cellular models for disease modelling. They have been used successfully over the past decade for Parkinson’s disease (PD) research and drug development. The three-dimensional structure and multicellular composition allow disease research under more physiological conditions than is possible with conventional 2D cellular models. However, there are concerns in the field regarding the organoid batch-to-batch variability and thus the reproducibility of the results. In this manuscript, we generate multiple independent midbrain organoid batches derived from healthy individuals or GBA-N370S mutation-carrying PD patients to evaluate the reproducibility of the GBA-N370S mutation-associated PD transcriptomic and metabolic signature as well as selected protein abundance. Our analysis shows that GBA-PD-associated phenotypes are reproducible across organoid generation batches and time points. This proves that midbrain organoids are not only suitable for PD in vitro modelling, but also represent robust and highly reproducible cellular models.

2025-07-08 | GSE287566 | GEO

Transcriptomic analysis of WT and POLG mutator macrophages

Project description:The goal of this study was to characterize gene expression profiles of wild-type (WT) and POLG D257A/D257A mutator (POLG mutator) macrophages at rest and 6 hours after lipopolysaccharide (LPS) challenge.

2021-04-13 | GSE171960 | GEO

RNA-seq of human midbrain organoid models of Parkinson's Disease

Project description:RNA-seq of human midbrain organoid models of Parkinson's Disease

| PRJEB45026 | ENA

scRNA-seq of Human midbrain organoids differentiated from WTSIi018-B-1 (healthy) and EDi001-B (Parkinson's Disease) iPSCs

Project description:Day 49 organoid differentiation of midbrain organoids

2023-01-01 | E-MTAB-12339 | biostudies-arrayexpress

Transcriptome profiling of DA neurons, human midbrain-like organoids and prenatal midbrain

Project description:Recent advances in three dimensional (3D) culture systems have led to the generation of brain organoids that share resemblance to different parts of the human brains; however, a 3D organoid model of the midbrain that contains functional midbrain dopaminergic (mDA) neurons has not been reported. In this study, we develop a method to differentiate human PSCs into a large multicellular organoid-like structure that contains distinct layers of neuronal cells with a transcriptomic profile that resembles human prenatal midbrain. Importantly, we detected electrically active and functionally mature mDA neurons, and dopamine production in our 3D midbrain-like organoids (MLOs). In contrast to human mDA neurons generated using non-3D methods or in the MLOs generated from mouse embryonic stem cells, our human MLOs uniquely produced neuromelanin-like granules that were structurally similar to those isolated from human substantia nigra tissues. Thus our MLOs bearing features of the human midbrain may provide a novel tractable in vitro system to study the human midbrain and its related diseases.

2016-08-24 | E-MTAB-4868 | biostudies-arrayexpress

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