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Expression analysis of neuronal differentiation of single mutants UBE3A/PHLDA2/SLC22A18 and double mutant PHLDA2/SLC22A18 cells

ABSTRACT: Expression analysis of neuronal differentiation of single mutants UBE3A/PHLDA2/SLC22A18 and double mutant PHLDA2/SLC22A18 cells

PROVIDER: PRJEB58997 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10783357.fastq.gz	Fastqsanger.gz
	ERR10783358.fastq.gz	Fastqsanger.gz
	ERR10783359.fastq.gz	Fastqsanger.gz
	ERR10783360.fastq.gz	Fastqsanger.gz
	ERR10783361.fastq.gz	Fastqsanger.gz

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Expression analysis of neuronal differentiation of single mutants UBE3A/PHLDA2/SLC22A18 and double mutant PHLDA2/SLC22A18 cells

Project description:Transcriptome analysis of UBE3A, PHLDA2, SLC22A18 and PHLDA2/SLC22A18 mutants during neuronal differentiation

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Expression analysis of neuronal differentiation of HOXA6/HOXB6/UBE3A mutants cells

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Expression analysis of neuronal differentiation of HOXA6/HOXB6/UBE3A mutants cells

Project description:Expression analysis of neuronal differentiation of HOXA6/HOXB6/UBE3A mutants cells

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Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids.

Project description:Angelman syndrome is a neurodevelopmental disorder caused by (epi)genetic lesions of maternal UBE3A. Research has focused largely on the role of UBE3A in neurons due to its imprinting in that cell type. Yet, evidence suggests there may be broader neurodevelopmental impacts of UBE3A dysregulation. Human cerebral organoids can investigate these understudied aspects of UBE3A as they recapitulate diverse cell types of the developing human brain. We performed single-cell RNA-sequencing on organoids to reveal the effects of UBE3A disruption on cell type-specific transcriptomic alterations and compositions. In the absence of UBE3A, progenitor proliferation and structures were disrupted while organoid composition shifted away from proliferative cell types. We observed impacts on non-neuronal cells including choroid plexus enrichment. Furthermore, EMX1+ cortical progenitors were negatively impacted, disrupting corticogenesis, and potentially delaying neuron maturation. This work reveals novel impacts of UBE3A on understudied cell types and related neurodevelopmental processes and elucidates potential new therapeutic targets.

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Ube3a-ATS characterization with strand-speicific microarray

Project description:This strand-specific array is performed to characterize expression features of Ube3a-ATS, including its imprinting status, its exon-intron structure, its transcriptional initiation and termination site as well as its polyadenylation status. The array contains reverse-complementary probes detecting transcripts from both strands and therefore we are able to pick up signal from both Ube3a sense and antisense. By comparing wild-type with various mutants, and total RNA with polyA RNA, we concluded that Ube3a-ATS is a paternally imprinted gene covering the whole gene body of Ube3a in the antisense orientation. It does not have an obvious exon-intron structure. Its transcription initiates at Snrpn major promoter and terminates ~40kb upstream of Ube3a transcriptional start site. Total RNA from Snrpn-Ube3a maternal deletion mutant (del s-u/+), its wild-type littermate, paternal deletion mutant and its wildtype littermate were analyzed. Mutant mice with S-U maternal deletion and Snrpn promoter paternal deleiton which leads to depletion of Ube3a-ATS (del s-u/0.9 and del s-u/4.8) were also analyzed. polyA RNA was purified from the sample 2 and sample 4. All eight samples were hybridized to the custom 8X60k Agilent CGH array.

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Ube3a-ATS characterization with strand-speicific microarray

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Bulk RNA-sequencing of pigs with UBE3A maternal deletion [Pig_Cortex_bulkRNAseq]

Project description:Angelman syndrome is a neurodevelopmental disorder caused by the loss of the maternal allele of the ubiquitin-protein ligase E3A (UBE3A) gene. UBE3A is imprinted with maternal-allelic expression in neurons of the central nervous syndrome (CNS) and biallelically expressed in other cell types. Consequently, in Angelman syndrome, UBE3A is absent in CNS neurons and reduced by half in other cells. Comparing both bulk and single nuclei RNA-sequencing, we show that gene expression is dysregulated in neuronal subtypes in the frontal cortex of pigs with a UBE3A maternal deletion.

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Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids.

Project description:Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids.

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