Ontology highlight
ABSTRACT:
PROVIDER: PRJNA393895 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5818210_1.fastq.gz | Fastqsanger.gz | |||
| SRR5818210_2.fastq.gz | Fastqsanger.gz | |||
| SRR5818211_1.fastq.gz | Fastqsanger.gz | |||
| SRR5818211_2.fastq.gz | Fastqsanger.gz | |||
| SRR5818206_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Avian zygote activates only maternal allele to disburden high variation of supernumerary sperms contrary to mammal
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Project description:In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individual cells, from zygote to the cells of the late blastocyst, and also individual cells from the adult liver. Using first generation crosses between two distantly related mouse strains, CAST/Ei and C57BL/6, we determined the expression separately from the maternal and paternal alleles. We found that half of the genes were expressed by only one allele, randomly so that some cells would express the paternal allele, some the maternal and a few cell both alleles. We also observed the spread of the progressive inactivation of the paternal X chromosome. First generation mouse strain crosses were used to study monoallelic expression on the single cell level
2014-01-10 | E-GEOD-45719 | biostudies-arrayexpress
Project description:In the diploid genome, genes come in two copies, which can have different DNA sequence and where one is maternal and one is paternal. In a particular cell, a gene could potentially be expressed from both copies (biallelic expression) or only one (monoallelic). We performed RNA-Sequencing on individual cells, from zygote to the cells of the late blastocyst, and also individual cells from the adult liver. Using first generation crosses between two distantly related mouse strains, CAST/Ei and C57BL/6, we determined the expression separately from the maternal and paternal alleles. We found that half of the genes were expressed by only one allele, randomly so that some cells would express the paternal allele, some the maternal and a few cell both alleles. We also observed the spread of the progressive inactivation of the paternal X chromosome.
2014-01-10 | GSE45719 | GEO
Project description:Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos. We found that within < 12 h of fertilization, each individual cell undergoes global genome demethylation together with the rapid and global reprogramming of both maternal and paternal genomes to a highly opened chromatin state. This was followed by decreased openness after the late zygote stage. Furthermore, from the late zygote to the 4-cell stage, the residual DNA methylation is preferentially preserved on intergenic regions of the paternal alleles and intragenic regions of maternal alleles in each individual blastomere. However, chromatin accessibility is similar between paternal and maternal alleles in each individual cell from the late zygote to the blastocyst stage. The binding motifs of several pluripotency regulators are enriched at distal nucleosome depleted regions from as early as the 2-cell stage. This indicates that the cis-regulatory elements of such target genes have been primed to an open state from the 2-cell stage onward, long before pluripotency is eventually established in the ICM of the blastocyst. Genes may be classified into homogeneously open, homogeneously closed and divergent states based on the chromatin accessibility of their promoter regions among individual cells. This can be traced to step-wise transitions during preimplantation development. Our study offers the first single-cell and parental allele-specific analysis of the genome-scale chromatin state and DNA methylation dynamics at single-base resolution in early mouse embryos and provides new insights into the heterogeneous yet highly ordered features of epigenomic reprogramming during this process.
2017-06-16 | GSE78140 | GEO
Project description:The goal of the present study is to analyze the characteristics of maternal to zygotic transition (MZT) in Arabidopsis. The maternal-to-zygotic transition (MZT) is an essential developmental turning point during the alternation of generations in both plants and animals. In animals, early embryogenesis is maternally controlled and zygotic genome activation (ZGA) starts much later. However, in plants, the timing of MZT and parental contributions to the zygotic transcriptome remain unclear. To address above mentioned questions, we selected Arabidopsis as model plant for the analysis. Regarding to the characteristics of MZT, egg cells, embryos including spherical zygote, elongated zygote, 1-cell embryo and 32-cell embryo were isolated and collected for RNA sequencing. Hybrid zygotes at two representative stages from the reciprocal crosses between polymorphic Arabidopsis Columbia (Col) and Landsberg erecta (Ler) accessions were also sequenced for investigating the parental contributions. We demonstrate that plant MZT occurs during the zygote stage and is a two-step process, first involving rapid maternal transcript degradation and, second, large-scale de novo transcription. Parental contributions to the zygotic transcriptome are stage dependent over the course of zygote development; the spherical zygote is characterized by a maternally dominated transcriptome, whereas the elongated zygote genome shows equal parental contributions.
2019-05-12 | GSE121003 | GEO
Project description:Genetic aberrations of the maternal UBE3A allele, which encodes the E3 ubiquitin ligase E6AP, are the cause of Angelman syndrome (AS), an imprinting disorder. In most cases, the maternal UBE3A allele is not expressed. Yet, approximately 10 percent of AS individuals harbor distinct point mutations in the maternal allele resulting in the expression of full-length E6AP variants that frequently display compromised ligase activity. In a high-throughput screen, we identified cyanocobalamin, a vitamin B12-derivative, and several alloxazine derivatives as activators of the AS-linked E6AP-F583S variant. Furthermore, we show by cross-linking coupled to mass spectrometry that cobalamins affect the structural dynamics of E6AP-F583S and apply limited proteolysis coupled to mass spectrometry to obtain information about the regions of E6AP that are involved in, or are affected by, binding cobalamins and alloxazine derivatives. Our data suggest that dietary supplementation with vitamin B12 could be beneficial for AS individuals.
2024-05-09 | PXD048963 | Pride
Project description:We collected over 8000 mouse embryos of each developmental stage (zygote, 2-cell, 4-cell, 8-cell, morula, blastocyst) and performed tandem mass tag (TMT)-based quantitative mass spectrometry and identified nearly 5000 proteins for each stage. In-depth analysis indicates that protein expression profiles of zygote, morula and blastocyst show apparent difference from 2- to 8-cell embryos due to the maternal-totipotent-differentiation transition. We further identified novel factors and proved that they play important roles in determining pre-implantation embryo development
2015-12-10 | MSV000079417 | MassIVE
Project description:Fertilization constitutes a critical step in the plant life cycle during which the gamete genomes undergo reprogramming in preparation for embryogenesis. However, it is unclear whether and how DNA methylation that epigenetically regulates gene expression is reprogramed during fertilization. Here, we characterized DNA methylation patterns and investigated the function of DNA glycosylases in rice eggs, sperms and unicellular zygotes. We found that DNA methylation is extensively reprogramed at non-CG sites in euchromatin regions upon fertilization, which intensifies during early embryogenesis. Genetic and genomic analysis revealed that rice DNA glycosylase genes DNG702, DNG701 and DNG704 demethylate at distinct and complementary loci in egg, sperm, and zygote genomes and are required for zygotic gene expression and development. The results indicate that active demethylation takes place in the gametes and the zygote to reprogram DNA methylation and zygotic genome activation in plant.
2020-02-08 | GSE143923 | GEO
Project description:We analyzed the functions of BTG family proteins in maternal mRNA degradation in mouse oocytes. By comparing the degradation of transcripts in WT oocytes and KO oocytes, we are able to know the defects in maternal mRNA clearance in BTG4-deleted oocytes, and identified the BTG4 target genes in oocyte cyplasmic maturation. 2 WT oocyte samples at GV stage, 2 WT oocyte samples at MII stage, 2 Btg4-/- oocyte samples at GV stage and 2 Btg4-/- oocyte samples at MII stage?2 WT embryo samples at zygote stage, 2 WT embryo samples at 2-cell stage, 2 Btg4-/- embryo samples at zygote stage and 2 Btg4-/- embryo samples at 2-cell stage , and a WT GV oocyte, a WT MII oocyte, a Erk-/- GV oocyte and a Erk-/- MII oocyte are performed RNA sequencing.
2016-03-16 | E-GEOD-71257 | biostudies-arrayexpress