Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

PROVIDER: PRJNA939208 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23633839_1.fastq.gz	Fastqsanger.gz
	SRR23633839_2.fastq.gz	Fastqsanger.gz
	SRR23633840_1.fastq.gz	Fastqsanger.gz
	SRR23633840_2.fastq.gz	Fastqsanger.gz
	SRR23633841_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

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

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

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

| PRJNA777256 | ENA

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 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

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

| PRJNA776164 | ENA

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

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

Impact of KIF26A loss in human forebrain organoids

Project description: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.

2022-09-20 | GSE213330 | GEO

Impact of KIF26A loss in human forebrain organoids

Project description:Impact of KIF26A loss in human forebrain organoids

| PRJNA880567 | ENA