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Genomic analysis of human parthenogenetic haploid ESCs (hPGES), normal human ESCs(H9) and human forskin fibroblast

ABSTRACT: Genomic analysis of human parthenogenetic haploid ESCs (hPGES), normal human ESCs(H9) and human forskin fibroblast

PROVIDER: PRJNA320304 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3470674_1.fastq.gz	Fastqsanger.gz
	SRR3470674_2.fastq.gz	Fastqsanger.gz
	SRR3470675_1.fastq.gz	Fastqsanger.gz
	SRR3470675_2.fastq.gz	Fastqsanger.gz
	SRR3470676_1.fastq.gz	Fastqsanger.gz

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mRNA expression data from human parthenogenetic haploid ESCs (hPGES), normal ESCs (H9) and human fibroblast

Project description:Here we report the derivation of human haploid ESCs from parthenogenetic haploid embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES), normal human ESCs (H9) and human forskin fibroblasts and identified that these cells express conventional ESCs pluripotent markers and most maternally imprinted genes were down-regulated.

2016-07-13 | GSE80988 | GEO

DNA methylation data from human parthenogenetic haploid ESCs (hPGES), normal human ESCs(H9) and human forskin fibroblast

Project description:Here we report the derivation of human parthenogenetic haploid ESCs which contain only one set of chromosome. These two cell lines, which we designated hPGES1 and hPGES2, show conventional ESCs and parthenogenetic-derived DNA methylation state.

2016-07-13 | GSE80226 | GEO

CNV anlysis of human parthenogenetic haploid ESCs (hPGES)

Project description:The genomic DNA sample of hPGES were compared to UCSC Human genome19 by CNV data. The data confirmed that the human parthenogenetic haploid ESCs sustained normal genome integrity

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mRNA expression data from ESCs derived by polar body transfer reconstructed embryos (PBTESCs)

Project description:Here we report the derivation of human PBTESCs from polar body transfer resconstructed embryos. We used RNA-seq to compare the gene expression levels among human parthenogenetic haploid ESCs (hPGES)、normal human ESCs (H9) and human forskin fibroblasts and identified that these cells express conventional ESCs pluripotent markers and most maternally imprinted genes were down-regulated.

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Establishment of monkey imprinted differentially methylated regions map by comparative analysis of parthenogenetic haploid embryonic stem cells and sperms

Project description:Genomic imprinting is a important biological process, which leads to parental specific gene expressions. Improper gene imprinting results in several developmental abnormalities, cancer and other diseases. Studies in mice indicated genomic imprinting establishment relied on parental allele-specific DNA methylation during gametogenesis. Despite the fact that genomic imprinting is highly conserved in mammalian, the species specific pattern exists. Until now, except that of in mouse, informations about imprinting patterns is little, especially in primates. Through generation genome-wide 5mC and 5hmC profiles for two types of haploid genomes from rhesus monkeys, including parthenogenetic haploid ESCs ( PG ha ESCs) (derived from rhesus monkey parthenogenetic embryos) and sperms. We clearly characterized and distinguished methylome (5mC) from hydroxymethylome (5hmC)(which can not discriminate from methylome in traditional bisulfite (BS) sequencing) in haploid genomes. Based on these information, we determined distribution patterns of 5mC and 5hmC in ha ESCs and sperms. Interestingly, both 5hmC levels and distribution patterns were similar in ha ESCs and sperms, and 5hmC which is enriched in the regions with low 5mC frequency. Meanwhile through comparing DNA methylation and hydroxymethylation status between sperms and ha ESCs, we first provided a fundamental information of monkey imprinted differentially methylated regions (DMRs) distribution in monkey chromosomes. Second, we observed that DMRs did not overlap with hydroxymethylated regions (DMR or DhMR), suggesting that establishment of imprinted regions was not interfered by 5hmC. Our results demonstrate DNA methylation profiling of PG ha ESCs and sperms can be uesed as a powerful and effective method to map and characterize imprinted regions in non-human primates genome.

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G2/M transition for stabilizing mouse haploid ESCs: CGH

Project description:To test genome stability of the parthenogenetic haploid embryonic stem cells, we performed array comparative genomic hybridization (aCGH) analysis.

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Transcriptional regulation of tDNA in H9 ESCs

Project description:The localization of Pol III, TFIIIB, and TFIIIC in untreated H9 ESCs and after 48 hours of 50ng/mL Activin A treatment was determined by ChIP-seq.

2020-02-02 | GSE94418 | GEO

Homo sapiens

Project description:mRNA expression data from human parthenogenetic haploid ESCs (hPGES), normal ESCs (H9) and human fibroblast

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Project description:To search for factors regulating paternally imprinted genes (PEGs), we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid parthenogenetic ESCs. This by staining a pooled CRISPR library with a PEG10 antibody and next FACS-sorted for cells that presented de-novo PEG10 expression.

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