Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Impact of KIF26A loss in human forebrain organoids

ABSTRACT: KIF26A is an unconventional kinesin that lacks motor activity. To characterize its role in brain development, we generated KIF26A knock-out iPSC lines and differentiated forebrain organoids. We performed single cell RNA sequencing at Day 60 and Day 80 to compare between control and KIF26A-deleted organoids at the molecular level, which revealed cell type-specific transcriptional changes in MAPK, MYC and E2F pathways.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213330 | GEO | 2022/09/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

Project description: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.

2024-08-04 | GSE273941 | GEO

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

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

| PRJNA1144131 | ENA

Genome-wide gene expression profiling post PCCB knockdown in human forebrain organoids

Project description:We established PCCB knockdown human induced pluripotent stem cell (hiPSC) line using CRISPR interference (CRISPRi). The established PCCB knockdown and control hiPSCs were then used to generate human forebrain organoids (hFOs). On day 60 of organoid culture, PCCB knockdown and control hFOs were randomly selected for RNA-sequencing (RNA-seq). We found that differentially expressed genes (DEGs) affected by PCCB knockdown were enriched with GABAergic synapse, synaptic vesicle cycle, neurotransmitter transport, forebrain development, axon development, synaptic organization, and calcium signaling pathways. The DEGs were also significantly overlapped with schizophrenia (SCZ)-associated genes, including genes dysregulated in brains or organoids derived from SCZ patients, and genes reported in SCZ GWAS.

2023-05-02 | GSE226233 | GEO

Proteome and secretome analysis of human dorsal forebrain organoids reveals a time-dependent shift in the abundance of cell adhesion and extracellular matrix proteins

Project description:Temporal dynamics of prenatal brain development are influenced by changes in the microenvironment. Particularly, extracellular proteins contribute to the dynamic niche that balances neural stem cell proliferation and differentiation. Here, we present a resource for proteome and secretome analysis of human induced pluripotent stem cell-derived dorsal forebrain organoids over the early developmental period. We used liquid chromatography-mass spectrometry to identify proteins found in whole organoid and secreted proteins at days 20, 35, and 50 of dorsal forebrain organoid differentiation. We show that the whole organoid proteome demonstrates progression in the neurodevelopmental trajectory with reduced proliferation and increased neural differentiation over time. However, secretome analysis revealed a unique signature for developmental progression. Cell adhesion molecules are enriched in the secretome of day 35 organoids, while secretome of day 50 organoids is enriched with extracellular matrix proteins, demonstrating a change in the extracellular interactions over time of organoid differentiation and maturation. We, therefore, show the relevance of secretome analysis for the thorough study of extracellular matrix-related proteins and the importance of time course study of neural organoids to understand the subtle changes that guide human neurodevelopment.

2024-05-27 | MSV000094878 | MassIVE

Genome-wide gene expression prolifing post-valproic acid exposure in human forebrain organoids

Project description:Human forebrain organoids (day 42) derived from U1M and U2F iPS cell lines were exposed with or without 1 mM valproic acid (VPA) for 72h. Organoids were then randomly selected for RNA sequencing, we found that differentially expressed genes (DEGs) induced by VPA exposure that shared in both U1M and U2F were enriched with neural development, synaptic transmission, calcium and potassium signaling pathways. The DEGs were also significantly enriched with autism spectrum disorder (ASD)-associated genes, including genes dysregulated in brains or organoids derived from ASD patients, and known ASD risk genes, as well as genes in ASD risk-associated gene coexpression modules.

2021-11-05 | GSE187006 | GEO

Single cell RNA-seq post valproic acid exposure in human forebrain organoids

Project description:Human forebrain organoids (day 50) derived from U1M and U2F iPS cell lines were exposed with or without 1 mM valproic acid (VPA) for 72h. Organoids were then used for single cell RNA sequencing (scRNA-seq). Through data processing, ten major cell types including astrocyte, choroid plexus, endothelia, intermediate progenitor cells, medial ganglionic eminence, radial glia, immature neuron, excitatory and inhibitory neuron, and microglia-like cells were identified. We found that VPA affected gene expression in choroid plexus, excitatory neuron, immature neuron, and medial ganglionic eminence cells. The cell type-specific DEGs were enriched with mitotic nuclear division, multiple neuronal functions, and response to type I interferon and virus.

2021-10-31 | GSE186814 | GEO

Impact of KIF26A loss in human forebrain organoids

Project description:Impact of KIF26A loss in human forebrain organoids

| PRJNA880567 | ENA

Gene expression profilling of day 30 cerebral organoids at the single cell level

Project description:To characterize cerebral organoids generated using STEMdiff Dorsal Forebrain Organoid Differentiation Kit were flash frozen on Day 30, we performed single cell RNA sequencing

2024-12-19 | GSE280812 | 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