Transcriptome characterization of embryogenesis at a single cell resolution [Panagrellus redivivus]
Ontology highlight
ABSTRACT:
ORGANISM(S): Panagrellus redivivus
PROVIDER: GSE86175 | GEO | 2019/08/29
REPOSITORIES: GEO
Similar Datasets
Project description:By collecting and processing individual embryonic cells from sequentially older embryos we have generated the first single cell transcriptome dataset describing embryogenesis from the fertilizaed zygote through to the penultimate cell division for most founder cell lines.
2023-03-22 | GSE83523 | GEO
Project description:By collecting and processing individual embryonic cells from sequentially older embryos we have generated the first comparative single cell transcriptome dataset describing embryogenesis.
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Project description:Analysis of DNA Methylation in Sperm, egg cell, fertilized zygote and preimplantation embryonic cells
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Project description:The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, while the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells, and pollen vegetative cells from rice, and identified transcripts for ~36,000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions and their contributions to zygote and seed development. The gene expression profiles of the three gametic cells, egg cell (EC), sperm cell (Sp) and vegetative cell (Ve) were compared via RNA-seq using three biological replicates for each. Differential expression (DE) analysis was performed using edgeR and the resulting DE genes were assessed for Gene Ontology term enrichment.
2013-10-31 | E-GEOD-50777 | biostudies-arrayexpress
Project description:During animal development, a fertilized egg is initially under the control of maternal products and only starts zygotic transcription after several cell divisions. In animals such as Xenopus, zebrafish and Drosophila, a massive increase in zygotic transcription occurs during the mid-blastula transition (MBT), when cells shift from rapid, synchronous cell divisions without gap phases to prolonged asynchronous divisions. Before MBT, only a few so-called pre-MBT genes are expressed. How transcription is set up during these early stages is poorly understood. For example, paused RNA Polymerase (Pol II) is frequently found at developmental control genes in mammalian embryonic stem cells and Drosophila embryos but when Pol II pausing is first established in the embryo is unknown. We have analyzed the genome-wide Pol II occupancy during the maternal-to-zygotic transition in hand-staged Drosophila embryos. The results show that massive Pol II recruitment and pausing is established during MBT. The ~100 genes that are transcribed before MBT are particularly short, consistent with a need for rapid transcription during these early cell divisions. Remarkably, most of these genes are transcribed without Pol II pausing and this correlates with a TATA-enriched promoter type. This suggests that distinct strategies are used for activation in the early Drosophila embryo and this may reflect general dynamic properties of promoters used throughout development. Mnase-seq in staged Drosophila embryos
2013-07-26 | E-GEOD-41686 | biostudies-arrayexpress
Project description:During animal development, a fertilized egg is initially under the control of maternal products and only starts zygotic transcription after several cell divisions. In animals such as Xenopus, zebrafish and Drosophila, a massive increase in zygotic transcription occurs during the mid-blastula transition (MBT), when cells shift from rapid, synchronous cell divisions without gap phases to prolonged asynchronous divisions. Before MBT, only a few so-called pre-MBT genes are expressed. How transcription is set up during these early stages is poorly understood. For example, paused RNA Polymerase (Pol II) is frequently found at developmental control genes in mammalian embryonic stem cells and Drosophila embryos but when Pol II pausing is first established in the embryo is unknown. We have analyzed the genome-wide Pol II occupancy during the maternal-to-zygotic transition in hand-staged Drosophila embryos. The results show that massive Pol II recruitment and pausing is established during MBT. The ~100 genes that are transcribed before MBT are particularly short, consistent with a need for rapid transcription during these early cell divisions. Remarkably, most of these genes are transcribed without Pol II pausing and this correlates with a TATA-enriched promoter type. This suggests that distinct strategies are used for activation in the early Drosophila embryo and this may reflect general dynamic properties of promoters used throughout development. ChIP-seq for Pol II, TBP, H3K4me3, H3K27me3 and H3Ac in Drosophila embryos
2013-07-26 | E-GEOD-41700 | biostudies-arrayexpress
Project description:gp130Act cDNA was PCR-amplified and inserted into a plasmid containing the 12.4-kb Villin promoter. The 15.7-kb expression cassette was excised by PmeI digestion, purified, and injected into fertilized C57BL/6 oocytes to obtain founder mice, two of which transmitted the gp130Act transgene. Small intestinal crypts were isolated from WT and villin-gp130Act Tg small intestines. Total RNA was isolated from the isolated crypts using the RNeasy Mini kit (Qiagen) and used for microarray analysis.
2015-02-21 | E-MTAB-2400 | biostudies-arrayexpress
Project description:The formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, while the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells, and pollen vegetative cells from rice, and identified transcripts for ~36,000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions and their contributions to zygote and seed development.
2013-10-31 | GSE50777 | GEO
Project description:In vitro culture of preimplantation mouse embryos is associated with changes in gene expression. It is however not known if the method of fertilization affects the global pattern of gene expression. We compared gene expression and development of mouse blastocysts produced in vitro (IVF), vs. blastocysts fertilized in vivo and cultured in vitro from the zygote stage (IVC), vs. control blastocysts flushed out of the uterus on post coital day 3.5. The global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip.
2007-05-06 | E-MEXP-1030 | biostudies-arrayexpress
Project description:The epigenomes of mammalian sperm and oocytes, characterized by gamete-specific 5-methylcytosine (5mC) patterns, are reprogrammed in early embryogenesis to establish full developmental potential. It is broadly accepted that the paternal genome is actively demethylated in the zygote while the maternal genome undergoes passive demethylation thanks to DNA replication over the subsequent cleavage divisions. Here we reveal that both maternal and paternal genomes undergo widespread active and passive demethylation in the pronuclear zygote before the first mitotic division. Whereas the passive demethylation requires DNA replication, the active demethylation relies on enzymatic oxidation of 5mC, as deletion of the DNA dioxygenase, Tet3, but not the inhibition of replication, blocks the active demethylation. At actively demethylated loci, 5mCs appear to be processed to unmodified cytosines in a manner independent of the DNA glycosylase TDG. These observations suggest the occurrence of genuine active demethylation in both parental genomes following fertilization. An extra supportive Tet3 knock-out female pronuclear sample related to experiment Series GSE56650.
2016-09-01 | E-GEOD-60777 | biostudies-arrayexpress