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Reduced representation bisulfite sequencing (RRBS) of haploid, diploid and triploid hESCs

ABSTRACT: Reduced representation bisulfite sequencing (RRBS) of haploid, diploid and triploid hESCs

PROVIDER: PRJEB51174 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR8958130.fastq.gz	Fastqsanger.gz
	ERR8958131.fastq.gz	Fastqsanger.gz
	ERR8958122.fastq.gz	Fastqsanger.gz
	ERR8958132.fastq.gz	Fastqsanger.gz
	ERR8958123.fastq.gz	Fastqsanger.gz

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Reduced representation bisulfite sequencing (RRBS) of haploid, diploid and triploid hESCs

Project description:To test the differences in genome-wide DNA methylation signatures of haploid, diploid and triploid hESCs, we extracted genomic DNA from these cells and performed RRBS.

2023-05-04 | E-MTAB-11478 | biostudies-arrayexpress

Differential gene expression profilings between diploid and triploid Fujian Oyster

Project description:The systematic deep sequencing analysis provided a comprehensive understanding of the transcriptome complexity of 2n and 3n Fujian oyster. This information broadens our understanding of the mechanisms of C.angulata polyploidization and contributes to molecular and genetic research by enriching the oyster database. This is the first report on genome-wide transcriptional analysis of adductor muscle of diploid and triploid Fujian oyster and has demonstrated triploid oysters are morphologically almost identical to their diploid counterparts, but have faster growth, due to the reorientation of energetic allocation from gametogenesis to somatic investment. This study provides a foundation for further analysis of the gene expression patterns and signaling pathways which regulate the molecular mechanisms of diploid and triploid oyster.

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A transcriptomic analysis of diploid and triploid Atlantic salmon lenses with and without cataracts

Project description:To avoid negative environmental impacts of escapees and potential inter-breeding with wild populations, the Atlantic salmon farming industry has and continues to extensively test triploid fish that are sterile. However, they often show differences in performance, physiology, behavior and morphology compared to diploid fish, with increased prevalence of vertebral deformities and ocular cataracts as two of the most severe disorders. Here, we investigated the mechanisms behind the higher prevalence of cataracts in triploid salmon, by comparing the transcriptional patterns in lenses of diploid and triploid Atlantic salmon, with and without cataracts. We assembled and characterized the Atlantic salmon lens transcriptome and used RNA-seq to search for the molecular basis for cataract development in triploid fish. Transcriptional screening showed only modest differences in lens mRNA levels in diploid and triploid fish, with few uniquely expressed genes. In total, there were 165 differentially expressed genes (DEGs) between the cataractous diploid and triploid lens. Of these, most were expressed at lower levels in triploid fish. Differential expression was observed for genes encoding proteins with known function in the retina (phototransduction) and proteins associated with repair and compensation mechanisms. The results suggest a higher susceptibility to oxidative stress in triploid lenses, and that mechanisms connected to the ability to handle damaged proteins are differentially affected in cataractous lenses from diploid and triploid salmon.

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RNA-seq of diploid and triploid parthenogenetic human embryonic stem cells

Project description:A comparison between diploid and triploid human embryonic stem cells. Characterization of triploid human embryonic stem cells and investigation of triploidy's effects on human development.

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Responses to ethanol in haploid and diploid strain

Project description:Diploid and haploid strains often exhibit different tolerance to variety of stresses. Transcriptome of acclimation to ethanol stress in diploid and haploid strain of Saccharomyces cerevisiae was analyzed. We analyzed transcriptome profiles of diploid and haploid strains in the presence of ethanol.

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Expression data from haploid and diploid epiblast stem cells

Project description:Haploid pluripotent stem cells, such as haploid embryonic stem cells (haESCs), facilitate the genetic study of recessive traits. In vitro, fish haESCs maintain haploidy in both undifferentiated and differentiated states, but whether mammalian haESCs can preserve pluripotency in the haploid state has not been tested. Here, we report that mouse haESCs can differentiate in vitro into haploid epiblast stem cells (haEpiSCs), which maintain an intact haploid genome, unlimited self-renewal potential, and durable pluripotency to differentiate into various tissues in vitro and in vivo. Mechanistically, the maintenance of self-renewal potential depends on the Activin/bFGF pathway. We further show that haEpiSCs can differentiate in vitro into haploid progenitor-like cells.

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Differential gene expression profilings between diploid and triploid Fujian Oyster

2014-03-06 | E-GEOD-55610 | biostudies-arrayexpress

Candida glabrata haploid and diploid

Project description:Candida glabrata haploid and diploid

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Expression data from human triploid and diploid fibroblast cell cultures

Project description:Dosage compensation restores a balanced network of gene expression between autosomes and sex chromosomes in males (XY) and females (XX). In mammals, this is achieved by doubling the expression of X-linked genes in both sexes, together with X inactivation in females. X up-regulation may be controlled by DNA sequence based and/or epigenetic mechanisms that double the X output potentially in response to an autosomal counting factor. Human triploids with either one or two active X chromosomes (Xa) provide a mean to test X chromosome expression in the presence of three sets of autosomes, which will help understand the underlying mechanisms of X up-regulation. We measured whole genome gene expression in human triploid cell cultures with either one or two active X. We found that overall X-linked gene expression is not tripled in the presence of three sets of autosomes. However, in triploid cells with a single active X chromosome, its expression is adjusted upward, presumably by an epigenetic mechanism that senses the active X-autosome ratio. Six human XXX triploid fibroblast clones with either one or two active X, three XYY triploid fibroblast cultures, and two male (XY) and two female (XaXi) control diploid fibroblast cultures were selected for RNA extraction and hybridization on Affymetrix whole genome expression arrays (HG-U133 2.0 plus chip). Probe labeling, array hybridization and scanning were done by the University of Washington Microarray Center.

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