Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-54112
PROVIDER: PRJNA235198 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1118400_1.fastq.gz | Fastqsanger.gz | |||
| SRR1118400_2.fastq.gz | Fastqsanger.gz | |||
| SRR1118401_1.fastq.gz | Fastqsanger.gz | |||
| SRR1118401_2.fastq.gz | Fastqsanger.gz | |||
| SRR1118402_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:ZNF804A transcriptome networks in differentiating human neurons derived from induced pluripotent stem cells
2025-01-24 | E-GEOD-54112 | ExpressionAtlas
Project description:Large-scale genomic screenings greatly advanced our understanding of the genetic basis of schizophrenia. However, how this translates into neurobiological functioning is not clear. Therefore, we aimed to characterize the function of robust susceptibility gene zinc finger protein 804A (ZNF804A), using a model system of relevant cell type and neurodevelopmental timepoint. Based on previous findings, we hypothesized a role for ZNF804A in local protein translation. CRISPR/Cas9-mediated mutation of the risk gene led to increased synapse formation in human induced pluripotent stem cell (hiPSC)-derived developing glutamatergic forebrain neurons as assessed by high-content confocal imaging. Further, mass spectrometry analysis showed an increased recruitment of ribosomes to mutation neurites. Surface sensing of translation (SUnSET) screening complemented this by demonstrating an increased efficiency of local protein synthesis. Overall, these results introduce a novel cellular function for ZNF804A in a model system relevant to schizophrenia, uncovering some aspects of its neurobiology. Ultimately, findings of this study may aid to identify common mechanisms of susceptibility genes.
2026-03-31 | PXD047788 | Pride
Project description:ZNF804A was amongst the first genes robustly associated with schizophrenia based on findings from large-scale genomic studies. Previous research has implicated ZNF804A inthe regulation of gene expression and synaptic function, but the role this gene plays inneurodevelopment and in relation to schizophrenia pathogenesis remains unclear. To study the function of this gene during neurodevelopment, we generated isogenichuman induced pluripotent stem cells (hiPSCs) with reduced ZNF804A expression, differentiated them into developing cortical glutamatergic neurons and studied theirtranscriptomic, synaptic and protein signatures. Mutant neurons showed modest changes in gene expression. However, high-content confocal imaging revealed increased excitatory synapse density in mutant neurons. Cell-compartment specific proteomic analysis further revealed that mutant neurons had higher levels of ribosomal andtranslational proteins in their neurites, and high-content imaging confirming increased local protein synthesis efficiency. Overall, these results demonstrate that in human developing cortical glutamatergic neurons, ZNF804A regulates excitatory synapse formation potential via increased local protein translation.
2024-01-30 | GSE254523 | GEO
Project description:The goal of this project is to study transcriptome change by knocking down ZNF804A, a schizophrenia and bipolar disorder candidate gene, in early neurons derived from iPSCs. Neural progenitor cells (NPCs) were developed from human induced pluripotent stem cells (iPSCs) and transduced by two independent shRNA vectors targeting ZNF804A, a schizophrenia and bipolar disorder candidate gene. After recovery and selection in puromycin, neuronal differentiation was induced. After 14 days, RNA was recovered and analyzed by RNA-seq. The expression profiles were compared with NPCs that were transduced with scrambled control vectors. This corresponds to controls 1-3 and KD 1-3, which was carried out on a male iPSC line. Scramble 1 and 2 and KD1 and 2 are technical replicates. Scrambled 3 and KD 3 were carried out on an independent NPC culture. For control 4 and KD4, neuronal differentiation was induced, and on day 10 the cells were transduced with the same ZNF804A KD and scrambled control vectors used for scrambled control 3 and KD3. In addition, this last set was carried out on a female iPSC line
2014-07-01 | E-GEOD-54112 | biostudies-arrayexpress
Project description:As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms were seen during the transition from pluripotent stem cells to early differentiating neurons. A number of genes that undergo radical changes in expression during this transition include candidates for schizophrenia (SZ), bipolar disorder (BD) and autism spectrum disorders (ASD) that function as transcription factors and chromatin modifiers, such as POU3F2 and ZNF804A, and genes coding for cell adhesion proteins implicated in these conditions including NRXN1 and NLGN1. In addition, a number of novel lncRNAs were found to undergo dramatic changes in expression, one of which is HOTAIRM1, a regulator of several HOXA genes during myelopoiesis. The increase we observed in differentiating neurons suggests a role in neurogenesis as well. Finally, several lncRNAs that map near SNPs associated with SZ in genome wide association studies also increase during neuronal differentiation, suggesting that these novel transcripts may be abnormally regulated in a subgroup of patients. Total RNAs were isolated from both iPS cells and differentiating neurons, and the sequenced material was pre-amplified using the NuGen Ovation amplification system. RNA-Seq libraries were prepared and carried out on Illumina HiSeq200.
2011-10-06 | E-GEOD-32625 | biostudies-arrayexpress
Project description:miRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes
| PRJNA155871 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE35671: Comparison of mRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes, biopsies from fetal, adult and hypertensive human hearts and primary cardiomyocytes GSE35672: miRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes Refer to individual Series
2012-02-10 | E-GEOD-35673 | biostudies-arrayexpress
Project description:Gene expression data from human induced pluripotent stem cells, induced pluripotent stem cell-derived human neural stem/progenitor cells, and iPSC-derived cerebral cortical neurons
| PRJNA260838 | ENA
Project description:To gain insight into the molecular regulation of human heart development, a detailed comparison of the mRNA and miRNA transcriptomes across differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes and biopsies from fetal, adult, and hypertensive human hearts was performed. Gene ontology analysis of the mRNA expression levels of the hiPSCs differentiating into cardiomyocytes revealed 3 distinct groups of genes: pluripotent specific, transitional cardiac specification, and mature cardiomyocyte specific. Hierarchical clustering of the mRNA data revealed that the transcriptome of hiPSC cardiomyocytes largely stabilizes 20 days after initiation of differentiation. Nevertheless, analysis of cells continuously cultured for 120 days indicated that the cardiomyocytes continued to mature toward a more adult-like gene expression pattern. Analysis of cardiomyocyte-specific miRNAs (miR-1, miR-133a/b, and miR-208a/b) revealed a miRNA pattern indicative of stem cell to cardiomyocyte specification. A biostatistitical approach integrated the miRNA and mRNA expression profiles revealing a cardiomyocyte differentiation miRNA network and identified putative mRNAs targeted by multiple miRNAs. Together, these data reveal the miRNA network in human heart development and support the notion that overlapping miRNA networks re-enforce transcriptional control during developmental specification. miRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes (days 0-120)
2012-02-10 | E-GEOD-35672 | biostudies-arrayexpress