Ontology highlight
ABSTRACT:
PROVIDER: PRJNA294663 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We developed a scalable assay permitting the simultaneous quantification of hundreds of proteins and the full transcriptome in thousands of individual cells from samples where cell number is limiting. The RNA Expression and Protein Sequencing assay (REAP-seq) uses DNA-labeled antibodies to permit DNA sequencing of both mRNA and antibodies in a single workflow using droplet microfluidics. We describe the development and validation of REAP-seq in human PBMCs, and use the assay to assess the costimulatory effects of an anti-CD27 agonist antibody in naïve CD8+ lymphocytes. Protein quantification using REAP-seq was more sensitive than parallel mRNA measurements and differentiated cell states with fewer analytes. Unbiased profiling of single cells without prior selection enabled identification and characterization of an unexpected cell type that would have been missed with population-averaged profiling methodologies.
2017-08-28 | GSE100501 | GEO
Project description:Accurate Protein Characterization and Quantification of Xenograft Tumors Requires Separating Human and Mouse Cells prior to Proteomics Profiling
2022-09-29 | PXD037070 |
Project description:Implantation is a milestone event during mammalian embryogenesis. Due to the extreme difficulty of obtaining in vivo human early post-implantation embryos, the gene regulatory network and epigenetics controlling human embryo implantation remains elusive. Here, combining an in vitro culture system for human post-implantation development and single-cell omics sequencing technologies, over 10,000 single cells at five representative stages of pre/post-implantation development were systematically analyzed. Unsupervised dimensionality reduction and clustering algorithm of the transcriptome data show stepwise implantation routes for the epiblast, primitive endoderm, and trophectoderm lineages, suggesting preparation for the establishment of a mother-to-offspring connection after implantation. Female embryos showed asynchronous progress of dosage loss of X chromosomes during implantation. Furthermore, using the single cell trio-Seq (scTrio-Seq) strategy, re-methylation of the genomes of all the three lineages was unambiguously revealed. Surprisingly, the genome re-methylation of PE lineage were much slower than both EPI and TE lineages during the implantation process, indicating distinct methylome features between EPI and PE although both of which were derived from ICM. Collectively, our work paves the way for understanding the complex molecular mechanisms that regulate human embryo implantation, informing new insights and future efforts in early embryonic development and reproductive medicine.
| EGAS00001003443 | EGA
Project description:Using single-cell genomics, we demonstrated that endogenous LINE-1s are mobilized in human pre-implantation embryos
2023-03-31 | GSE149472 | GEO
Project description:Members of the miR-371 cluster are of the earliest de novo synthesized by embryos and have important actions in mammalian reproduction. MiR-371a is secreted by embryos at the peri-implantation period and its release has been previously associated with poor embryo quality and lower implantation rates in women undergoing IVF. Here we investigated the potential biological role of miR-371a release in regards to embryonic implantation, and specifically the molecular effects that this miRNA exerts on the cells of the endometrial lining. Gene expression changes in endometrial cells upon miR-371a addition were therefore identified using large-scale genomic plattform that covers the whole human genome (Affymetrix).
2021-05-01 | GSE158998 | GEO
Project description:Mouse oocytes and embryos from the germinal vesicle (GV) stage to the blastocyst stage were collected and treated with acidic Tyrode’s solution to remove the zona pellucida. We used 42.5 oocytes or embryos per sample at each developmental stage and identified the proteome during mouse pre-implantation development by label-free quantification.
2025-05-22 | PXD059122 | JPOST Repository
Project description:Comprehensive quantitative proteomic study of human pre-implantation embryo stages reveal dynamic proteome landscape from M2, 8-cell and blastocyst stage, and during trophoblast stem cell (TS) differentiation. Identified key factors in early human embryos and lineage-specific trophoblast proteome profiles, correlated with transcriptomic analyses. This direct proteomic analysis provides a comprehensive analysis of the dynamic protein expression in human embryos during pre-implantation development and a powerful resource to enable further mechanistic studies on human trophoblast development and function.
2023-07-05 | MSV000092349 | MassIVE
Project description:Single-cell RNA-seq dataset of models of human embryo adhesion in a microfluidic platform (ADOC). Embryo adhesion represents the first step of implantation, yet understanding this process has been hindered by the lack of human in vitro platforms that replicate endometrial physiology. Here, we present a dual-channel microfluidic platform containing organoid-derived endometrial epithelium and primary stromal cells. Our model recapitulates important endometrial hallmarks including epithelial polarization, stromal decidualization, extracellular vesicle release, and hormone-induced receptivity. We tested its function by introducing mouse and human blastocysts and showed that embryos displayed features of initial adhesion. These included establishment of embryo-epithelial contacts initiated via the polar trophectoderm, inner cell mass repositioning, and lineage segregation. Moreover, human embryos secreted βhCG indicating a functional trophoblast. Thus, this work provides a platform to study key features of embryo adhesion and endometrial receptivity, and disorders affecting embryo-endometrium interactions.
2026-07-13 | E-MTAB-15842 | biostudies-arrayexpress
Project description:Implantation is a milestone event during mammalian embryogenesis. Implantation failure is a nonnegligible cause of human early pregnancy loss. Due to the extreme difficulty of obtaining in vivo human early post-implantation embryos, it remains elusive how the gene regulatory network and epigenetic mechanisms control human embryo implantation. Here, combining an in vitro culture system for human post-implantation development and single-cell omics sequencing technologies, over 8,000 individual cells from 65 human peri-implantation embryos were systematically analyzed. Unsupervised dimensionality reduction and clustering algorithm of the transcriptome data show stepwise implantation routes for the epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE) lineages, suggesting robust preparation for the proper establishment of a mother-to-offspring connection during implantation. Female embryos showed initiation of random X chromosome inactivation based on analysis of parental allele-specific expression of X chromosome-linked genes during implantation. Surprisingly, by the single-cell Trio-Seq (scTrio-Seq) analysis, the genome re-methylation of PE lineage was shown to be much slower than those of both EPI and TE lineages during implantation process, indicating distinct DNA methylome re-establishment features between EPI and PE although both of which were derived from inner cell mass (ICM). Collectively, our work paves the way for understanding the complex molecular mechanisms that regulate human embryo implantation, offering new insights and future efforts in early embryonic development and reproductive medicine.
2019-07-11 | GSE109555 | GEO
Project description:MicroRNAs (miRNAs) are important regulators of many biological functions, including embryo implantation and development. Recently, it is reported that miRNAs in biofluids are predictive for physiological and pathological processes. In this study, we aim to investigate whether the miRNAs secreted by human embryos in culture medium can be used as embryonic biomarkers. The culture media were prospectively collected from embryos of patients who underwent routine in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) at reproductive medicine center with informed consent. A high-throughput miRNA sequencing method was applied to detect the miRNAs profiles in culture media of embryos with different reproductive outcomes. Compared with embryos with failed pregnancy, the embryos with successful pregnancy secreted different miRNA profiles into the culture media. These differentially expressed miRNAs were predicted to be involved in multiple biological processes, cellular components and molecular functions. After bioinformatics analysis, 18 miRNAs were selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR) and droplet digital PCR (ddPCR). We found that the cleavage embryos with successful pregnancy presented decreased expression of hsa-miR-26b-5p and hsa-miR-21-5p in the culture media. Moreover, the Receiver Operating Characteristic (ROC) curve analysis indicated that hsa-miR-26b-5p and hsa-miR-21-5p could serve as potential biomarkers for reproductive outcomes. Together, our findings highlight the important predictive potential of miRNAs secreted by human embryos in culture media, which is meaningful for noninvasive embryo selection during IVF cycles.
2020-02-28 | GSE142824 | GEO