Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA-sequencing of 90-day old astrocyte conditioned medium treated forebrain organoids (ACMOs) and control forebrain organoids

ABSTRACT: The scRNA-seq analysis of 90-day old ACMOs and forebrain organoids reveals six well-defined major clusters. All cells were categorized into six distinct clusters: (1) deep layer subcortical projection neurons, (2) upper layer projection neurons, (3) intermediate progenitors, (4) radial glial cells, (5) dividing cells, (6) astrocytes. Both ACMOs and control organoids underwent a correct trajectory of cell diversification and contained a large diversity of progenitor and neuronal cell types belonging to the neuroectodermal lineage. Transcriptomic comparisons and pathway enrichment analysis were performed between control organoids and ACMOs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE273941 | GEO | 2024/08/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Single cell RNA-sequencing of 75-day old human H1 and H9 embryonic stem cell-derived cerebral organoids

Project description:The scRNA-seq analysis of 75 day old human cerebral organoids grown at the air-liquid interface (ALI-COs) reveals six well-defined major clusters. Cell-type and maturity markers define a (1) distinct population of deep layer subcortical projection neurons, (2) upper layer intracortical (callosal) projection neurons and intermediate progenitors, (3) ventricular and subventricular zone radial glial cells, (4) more mature upper and deep layer neurons, (5) interneurons and (6) actively dividing cells with intermediate progenitor and radial glia markers. In addition, the gene expression profile of these clusters corresponds with their expected functional characteristics appropriate to their maturity. Altogether, our data reflect a full repertoire of cortical neuronal and progenitor identities corresponding with the stages of cortical development in age-matched fetal brains.

2019-02-28 | GSE124174 | GEO

Virally Encoded Connectivity Transgenic Overlay RNA sequencing (VECTORseq) defines projection neurons involved in sensorimotor integration

Project description:Purpose: Establish a high-throughput method to transcriptionally define projection neurons, VECTORseq, that reimagines transgenes expressed by widely used retrogradely infecting viruses as multiplexed RNA barcodes that are detected in single-cell sequencing. Methods: mRNA profiles of adult mouse brains Conclusions: Retrograde viruses express mRNA at levels detectable in single-cell sequencing. Different transgenes can be multiplexed in a single sequencing run. VECTORseq identifies both cortical and subcortical projection neurons. VECTORseq defined new superior colliculus and zona incerta projection populations. Established a high-throughput method to transcriptionally define projection neurons, VECTORseq, that reimagines transgenes expressed by widely used retrogradely infecting viruses as multiplexed RNA barcodes that are detected in single-cell sequencing.

2021-12-02 | GSE189907 | GEO

Single cell analysis of iPSC-derived cortical organoids in biofunctionalized gelatin hydrogels

Project description:Human neural organoid models have become an important tool for studying neurobiology. In this work, we compared Matrigel to an N-cadherin peptide-functionalized gelatin methacryloyl hydrogel (termed GelMA-Cad) for culturing cortical neural organoids. Specifically, we compare five materials: (1) Matrigel, (2) GelMA-Cad with high crosslinker (HC), (3) GelMA-Cad with low crosslinker (LC), (4) GelMA HC and (5) GelMA LC. We determined that both mechanical properties and peptide presentation can tune cell fate and diversity in gelatin-based matrices during differentiation. Of particular note, cortical organoids cultured in GelMA-Cad produce higher numbers of neurogenic and ciliated radial glia and upper-layer excitatory neurons—an important population for modeling neurodegenerative disease—compared to GelMA and Matrigel controls.

2024-02-28 | E-MTAB-13828 | biostudies-arrayexpress

Epigenomic Diversity of Cortical Projection Neurons in the Mouse Brain

Project description:Neuronal cell types are classically defined by their molecular properties, anatomy, and functions. While recent advances in single-cell genomics have led to high-resolution molecular characterization of cell type diversity in the brain, neuronal cell types are often studied out of the context of their anatomical properties. To better understand the relationship between molecular and anatomical features defining cortical neurons, we developed Epi-Retro-Seq, a method that combined retrograde labeling with single-nucleus DNA methylation sequencing to link epigenomic properties of cell types to neuronal projections. We profiled 16,971 single neocortical neurons from 63 cortico-cortical and cortico-subcortical long-distance projections. Our results revealed unique epigenetic signatures of projection neurons that correspond to their laminar and regional location and projection patterns. The methylomes of 16,971 mouse neocortical neurons from 63 cortico-cortical (CC) and cortico-subcortical long-distance projections were analyzed using Epi-Retro-Seq, a method that combined retrograde tracing and single nucleus methylome sequencing.

2020-11-16 | GSE150170 | GEO

Expression changes in the prefrontal cortex after neurotransmission blocking of nucleus accumbens pathways

Project description:GSEA using both edgeR and voom statistics revealed that the ES of two types of corticothalamic neurons, CTX.Glt25d2-positive layer 5b and CTX.Ntsr1-positive layer 6 neurons, were downregulated by both NAc D1- and D2-RNB. In contrast, the ES of CTX.S100a10 corticostriatal neurons were upregulated and downregulated by NAc D1- and D2-RNB, respectively. These data show that cortical neurons are asymmetrically regulated by subcortical pathways in the mPFC-NAc-VP/SNr-MD/VD-mPFC circuit.

2019-01-03 | GSE124583 | GEO

Co-repressor CDYL confers forebrain identity to human cortical organoids by negatively regulating NNAT [ChIP-Seq]

Project description:Epigenetic regulation is essential for the normal development of human cerebral cortex, and its disruptions would lead to diverse neurodevelopmental disorders. The epigenetic co-repressor CDYL exhibits widespread expression across various cell clusters within the human embryonic cortex, yet its roles in this intricate process have remained elusive. Here, we show that CDYL is critical for cortical neurogenesis, and CDYL deficiency led to an augmentation in the generation of GABAergic neurons instead of cortical progenitors and neurons in the cortical organoid model. Combining analysis of bulk RNA-seq and ChIP seq, we identified NNAT as a significant CDYL target by H3K27me3 modification, crucial for the fate determination of neural stem cells within human cortical organoids, distinctly diverging from the murine cortex at a similar developmental stage. Collectively, our study sheds light on the critical function of CDYL in the maintenance of cortical neural stem cell fate commitment during human corticogenesis through the inhibition of NNAT expression.

2023-11-13 | GSE247086 | GEO

Co-repressor CDYL confers forebrain identity to human cortical organoids by negatively regulating NNAT [RNA-Seq]

2023-11-13 | GSE247084 | GEO

Transcription profiling of human dorsal forebrain organoids treated with Hyper-IL-6

Project description:Description: RNA-seq of total RNA isolated from dorsal forebrain organoids at days 50 and 55 of differentiation. The study aimed at investigating the effects of 5 or 10 days of Hyper-IL-6 exposure on transcriptional profiles of dorsal forebrain organoids.

2023-03-08 | E-MTAB-12702 | biostudies-arrayexpress

Project description:As cortical organoids consist of a heterogeneous population of cell-types, 6-month-old DM1 and Rett syndrome cortical organoids were subjected to single cell RNA-seq (scRNA-seq) analysis to determine which cell type(s) CELF2’s RNA targets are expressed in. Unsupervised clustering was implemented on the combined dataset of 8595 cells from control, DM600, and DM1200 cortical organoids that consisted of ~2865 cells per organoid line and ~17,575 reads per cell to identify genotype-specific clusters at 6-months post-differentiation. Uniform Manifold Approximation and Projection (UMAP) for dimension reduction revealed clear differences between control and DM1 organoids. From the expression of established cell-type specific gene markers, smaller sub-clusters were combined to represent four major cell classes: neural progenitors, intermediate neural progenitors, glutamatergic cortical neurons, and glial cells.

2022-06-30 | GSE201891 | GEO

Single-cell transcription profiling human dorsal forebrain organoids treated with Hyper-IL-6

Project description:We performed single-cell RNA sequencing of dorsal forebrain organoids at day 53 of differentiation upon treatment with Hyper-IL-6. The study aimed at investigation of the effects of Hyper-IL-6 on transcriptional profiles of dorsal forebrain organoids at single-cell level.

2023-03-08 | E-MTAB-12743 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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