Transcriptional profiling of mammalian preimplantation embryos
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ABSTRACT:
PROVIDER: PRJNA933618 | ENA |
REPOSITORIES: ENA
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Project description:We developed an adapted version of Smart-seq2, which we call Smart-seq+5', to capture both internal transcript fragments, as well as 5' transcript information, in mammalian preimplantation stages on a single-embryo level. Focussing specifically on transposable elements, we find many conserved patterns and features shared between mouse, pig, cow, rabbit and rhesus.
2025-01-19 | GSE225056 | GEO
Project description:Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our Comprehensive Solution of Ultrasensitive Proteome Technology to measure the proteomic profiles of oocytes and early embryos, and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatome data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts contribute to protein accumulation in blastocysts. Consequently, we identified several transcriptional regulators critical for early development in mice, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor quality embryos from over 100 patient-couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening new avenues for addressing human infertility.
2024-12-04 | GSE283213 | GEO
Project description:Landmark events occur in a coordinated manner during preimplantation development of the mammalian embryo, yet the regulatory network that orchestrates these events remains largely unknown. We delineated the regulons of Oct4, Sall4, and Nanog using morpholino (MO)-mediated gene knockdowns followed by microarray analysis of pooled embryos. 1-cell fertilized mouse embryos were injected with a morpholino and were collected at either 20 hours or at 44 hours after microinjection.
2012-11-09 | E-GEOD-42135 | biostudies-arrayexpress
Project description:Landmark events occur in a coordinated manner during preimplantation development of the mammalian embryo, yet the regulatory network that orchestrates these events remains largely unknown. We delineated the regulons of Oct4, Sall4, and Nanog using morpholino (MO)-mediated gene knockdowns followed by microarray analysis of pooled embryos.
2012-11-09 | GSE42135 | GEO
Project description:Preimplantation embryonic development is a dynamic, complex and precise regulated process to govern embryonic development and maintain embryo viability. The complete dynamics transcriptional activities during preimplantation development in the important domestic species goat is not available. Here, we performed RNA sequencing to establish a comprehensive transcriptional profiling of goat in vivo matured oocytes and preimplantation embryos. We found that the embryonic genome activation (EGA) in goat occurs at 16-cell stages, not previously defined at 8-cell stage, and showed much later EGA process compared to all other mammalian species. A total of 6,482 genes were identified to be significantly differentially expressed across all consecutive developmental stage comparisons and the important signaling pathways involved in each development transition were revealed. Additionally, we identified genes that appear to be transcribed only in a specific stage of development. Using weighted gene co-expression network analysis, we found 9 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the goat expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryo development. Our cross-mammalian species transcriptomic comparisons demarcated both conserved and goat specific features of preimplantation development.
2020-03-01 | GSE129742 | GEO
Project description:Differential gene expression in preimplantation embryos has been documented, but few focused studies have been done to compare differential expression in human embryos after embryonic genome activation and specifically how they relate to blastocyst development. We hypothesized that blastocyst stage embryos would differentially express genes in pathways important in cell division, mobilization, and processes important in embryo implantation including endometrial apposition, adhesion, and invasion. We analyzed gene expression in 6 preimplantation human embryos. Embryos studied were previously cryopreserved, supernumerary human embryos donated by couples who completed their family building through in vitro fertilization and had given specific consent for use in research. Embryos cryopreserved at the pronuclear stage were thawed and cultured to cleavage (Day 3) or blastocyst (Day 5) stage. Differential gene expression was first obtained through Affymetrix gene expression microarrays and then validated both in silico using the Gene Expression Omnibus and in vitro with RT-qPCR. Compared to cleavage stage embryos, blastocyst stage embryos differentially expressed 51 genes (p < 0.001), with overrepresentation in amoebiasis pathways and pathways in cancer.
2015-12-25 | GSE73856 | GEO
Project description:Transcriptional profiling of embryos lacking Flvcr1
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Project description:Sperm-derived tsRNAs could act as acquired epigenetic factors and contribute to offspring phenotypes. However, the roles of specific tsRNAs in early embryo development remain to be elucidated. Here, by using pigs as a research model, we probed the tsRNA dynamics during spermatogenesis and sperm maturation, and demonstrated the delivery of tsRNAs from semen-derived exosomes to spermatozoa. By microinjection of the antisense sequence into in vitro fertilized oocytes and subsequent single-cell RNA-sequencing of embryos, we identified a specific functional tsRNA group (Gln-TTGs) that participate in the early cleavage of porcine preimplantation embryos, probably by regulating cell cycle-associated genes. Thus, specific tsRNAs present in mature spermatozoa play significant roles during preimplantation embryo development.
2020-07-13 | PXD019054 | Pride
Project description:RNA-seq and ChIP-seq for H3K79me3 and H3K79me2 in mESCs and preimplantation embryos
2023-06-09 | GSE182744 | GEO
Project description:To investigate the importance of DNA damage checkpoint regulation in mammalian preimplantation embryos, we overexpressed wild type and mutant form of CHK1 kinase in mouse zygotes and performed high-throughput RNA-sequencing of zygotes, late 2-cell embryos and blastocysts. Transcriptome analysis revealed that zygotes are particular sensitive to the perturbation of Chk1 governed DNA damage checkpoint. However, once zygotes can overcome DNA damage checkpoint induced cell cycle arrest, they can still have normal development.
2021-05-04 | GSE163765 | GEO