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Transcriptome profiling of normal and DNMT3L-overexpressing human neurons [RNA-seq]

ABSTRACT: Transcriptome profiling of normal and DNMT3L-overexpressing human neurons [RNA-seq]

PROVIDER: PRJNA660028 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12541232_1.fastq.gz	Fastqsanger.gz
	SRR12541232_2.fastq.gz	Fastqsanger.gz
	SRR12541233_1.fastq.gz	Fastqsanger.gz
	SRR12541233_2.fastq.gz	Fastqsanger.gz
	SRR12541234_1.fastq.gz	Fastqsanger.gz

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Normal and DNMT3L-overexpressing human neurons

Project description:Normal and DNMT3L-overexpressing human neurons

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Transcriptome profiling of normal and DNMT3L-overexpressing human neurons [RNA-seq]

Project description:The objective of this study is to test the gene expression changes caused by DNMT3L overexpression in human neurons. The total RNA of each sample was extracted from the lentivirus infected, early differentiated human neuroprogenitors with ZsGreen (n=3) or DNMT3L (n=3) overexpression by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. Results: among 57 905 cleaned RNAs, 7983 RNAs were differentially expressed in DNMT3L overexpressing neurons compared with control neurons, with q-value ≤ 0.05. After limited the cut-off by adding |fold change| ≥ 1.5, the numbers of differential expressed RNAs lowered to 1073, with more down-regulation (590) than up-regulation (483). The differential expressed genes distributed in all chromosomes, also showing the pattern of more down-regulation than up-regulation in every chromosome except chromosome 21. Functional annotation with DAVID revealed the top functional groups including type I interferon signaling pathway and RNA and protein processing.

2020-08-29 | GSE157080 | GEO

Epigenome analysis of normal and DNMT3L-overexpressing human neurons [array]

Project description:Genome wide DNA methylation profiling of cultured fetal human neurons infected with lentivirus carrying DNMT3L or ZsGreen genes for 4days. The Illumina Infinium 850k Human MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in the infected cells. Samples included 3 control samples (ZsGreen) and 3 DNMT3L-overexpressing samples (DNMT3L).

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Epigenome analysis of normal and DNMT3L-overexpressing human neurons [array]

Project description:Epigenome analysis of normal and DNMT3L-overexpressing human neurons [array]

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Transcriptome profiling of wild type and DNMT3L-overexpressing Drosophila larvae brains

Project description:The objective of the study was to examine the gene expression changes caused by human DNMT3L overexpression in Drosophila melanogaster brains. There were 6 samples in total- C1, C2, C3, D1, D2, and D3. C1-C3 were larvae brains from the strain of elavC155-Gal4, which were used as the control group (C). D1-D3 were larvae brains from the strain with DNMT3L overexpression, which were bred by crossing the strains of elavC155-Gal4 and w/w;P(UAS-DNMT3L,w+)/Cyo;TM2/TM6B and used as the DNMT3L overexpressing group (D). The total RNA of each sample was extracted from 30 brains of the 3rd instar larvae of Drosophila by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. Results: among 17737 cleaned RNAs, 267 RNAs were differentially expressed in DNMT3L overexpressing group compared with control group, with q-value ≤ 0.05 and |fold change|≥2 , with more down-regulation (151) than up-regulation (116). They corresponded to 655 human homologous genes. The differential expressed genes distributed in all chromosomes. Functional annotation with GO and KEGG enrichment revealed the top functional groups including calcium ion transport, voltage gated channel, choilnergic synapse, serotonergic synapse, and drug metabolism.

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Transcriptome profiling of wild type and DNMT3L-overexpressing Drosophila larvae brains

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Transcription profiling of mpuse Dnmt3l-/+ (maternal methylation-deficient) vs normal 8.5dpc embryos

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