Revealing a coherent cell state landscape across single cell datasets with CONCORD
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ABSTRACT:
PROVIDER: PRJNA1304262 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed single-cell transcriptional profiling of Caenorhabditis elegans embryos to benchmark CONCORD, a dimensionality reduction and data integration framework for single-cell analysis. This dataset complements previously published late-stage embryogenesis transcriptomic studies by enriching for early-stage embryos through low-temperature culture conditions, enabling construction of a comprehensive, continuous map of the full embryogenesis process.
2025-08-28 | GSE305031 | GEO
Project description:We combined in vivo expressed GFP-tagged MEG-3 (GEI-12) with label-free quantitative proteomics to identify protein-protein interactions of MEG-3 in early C. elegans embryos.
2021-07-01 | PXD012852 | Pride
Project description:While non-mammalian embryos often rely on spatial pre-patterning, for decades it was
believed that blastomeres of mouse and human embryos were developmentally
equivalent. However, emerging evidence suggests early mouse and human
blastomeres differ in developmental potential. Here, using multiplexed and label-free
single-cell proteomics, we identify over three hundred asymmetrically abundant proteins
- many involved in protein degradation and transport - that divide mouse 2-cell stage
blastomeres into two distinct clusters, which we term alpha and beta. These
asymmetries intensify at the 4-cell stage and are detectable as early as the zygote.
Fertilisation acts as a trigger for this breaking of symmetry and sperm entry point
correlates with the gradient of proteome asymmetry. Perturbation of beta-enriched
proteins (Gps1, Nedd8) alters lineage segregation. Embryos derived from beta
blastomeres have more epiblast cells, while alpha blastomeres are associated with a
lower developmental potential. Human 2-cell embryos show similar clustering and
enrichment patterns, supporting conservation of this early asymmetry. Our findings
reveal a previously unrecognized proteomic pre-patterning triggered by fertilisation in
mammalian embryos, with implications for understanding totipotency and early lineage
bias.
2025-08-10 | MSV000098778 | MassIVE
Project description:Transcriptional profiling of early C. elegans embryos comparing control (N2) embryos with mes-2 mutant embryos at different developmental stages: 2E (24-40 cells), 4E (50-90 cells) and 8E stage (100-200 cells). Goal was to determine the effects of mes-2 loss on global gene expression as embryos transit from a developmentally plastic state (2E stage) to the onset of differentiation (8E stage). Our microarray data showed that early-expressed genes remain active, differentiation genes fail to reach wild-type levels in mes-2 mutant embryos at the 8E stage.
2009-05-26 | GSE14913 | GEO
Project description:Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect large amounts of cleanly staged C. elegans embryos by Fluorescent Activated Cell Sorting (termed eFACS). eFACS can in principle be applied to all embryonic developmental stages up to hatching. As a proof of principle we show that a single eFACS run routinely yields tens of thousands of almost perfectly staged one-cell embryos. Since in animals the earliest embryonic events are driven by post-transcriptional regulation, we combined eFACS with next-generation sequencing technology to systematically profile the embryonic expression of small, non-coding RNAs. We discovered a wealth of complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including miRNAs, during embryogenesis. Our data indicate that half of all known miRNAs are already expressed in the one-cell stage embryo and we also shed light on the expression and genomic organization of the previously under-appreciated 26G-RNAs. Together, our eFACS data suggest that the complexity of small RNA expression dynamics in animals is comparable to the expression dynamics of protein encoding genes. Various C. elegans embryo samples were generated: mixed embryos by traditional bleaching (Brenner, 1974), early embryos by eFACS (Stoeckius et al., in press). RNA was extracted and length fractionated. Small RNA was subjected to a 5'-dependent ligation protocol to add sequencing adapters. The small RNA samples were sequenced using the Illumina GA I & II.
2009-09-06 | E-GEOD-17153 | biostudies-arrayexpress
Project description:We combine in vivo expressed GFP-tagged proteins with quantitative proteomics to identify protein-protein interactions of selected key proteins involved in early C. elegans embryogenesis. Co-affinity purification of interaction partners for eight bait proteins resulted in a pilot in vivo interaction map of proteins with a focus on early development.
2016-02-29 | PXD002624 | Pride
Project description:Caenorhabditis elegans is one of the most prominent model systems to study embryogenesis. However, it has been impractical to collect large amounts of precisely staged embryos. Thus, early C. elegans embryogenesis has not been amenable to most modern high-throughput genomics or biochemistry assays. To overcome this problem, we devised a method to collect large amounts of cleanly staged C. elegans embryos by Fluorescent Activated Cell Sorting (termed eFACS). eFACS can in principle be applied to all embryonic developmental stages up to hatching. As a proof of principle we show that a single eFACS run routinely yields tens of thousands of almost perfectly staged one-cell embryos. Since in animals the earliest embryonic events are driven by post-transcriptional regulation, we combined eFACS with next-generation sequencing technology to systematically profile the embryonic expression of small, non-coding RNAs. We discovered a wealth of complex and orchestrated changes in the expression between and within almost all classes of small RNAs, including miRNAs, during embryogenesis. Our data indicate that half of all known miRNAs are already expressed in the one-cell stage embryo and we also shed light on the expression and genomic organization of the previously under-appreciated 26G-RNAs. Together, our eFACS data suggest that the complexity of small RNA expression dynamics in animals is comparable to the expression dynamics of protein encoding genes.
2009-09-06 | GSE17153 | GEO
Project description:To determine how the genome is packaged in C. elegans sperm, we isolated adult him-8(e1489) males and collected mature sperm (~99% purity). We utilized micrococcal nuclease digestion followed by paired-end sequencing (MNase-seq) to evaluate the presence of nucleosomes across the genome in sperm vs. early embryos. We found that the sperm genome retains nucleosomes genome-wide, comparable to wild-type early embryos.
2018-07-23 | GSE115705 | GEO
Project description:Transcriptional profiling of early C. elegans embryos comparing control (N2) embryos with mes-2 mutant embryos at different developmental stages: 2E (24-40 cells), 4E (50-90 cells) and 8E stage (100-200 cells). Goal was to determine the effects of mes-2 loss on global gene expression as embryos transit from a developmentally plastic state (2E stage) to the onset of differentiation (8E stage). Our microarray data showed that early-expressed genes remain active, differentiation genes fail to reach wild-type levels in mes-2 mutant embryos at the 8E stage. Two-condition experiment, wild type vs. mes-2 embryos. Biological replicates: 3 control replicates, 3 mes-2 replicates for each stage.
2010-05-18 | E-GEOD-14913 | biostudies-arrayexpress
Project description:Okazaki fragments were purified and sequenced from C. elegans embryos at various stages of development. The sequencing data was used to map the positions and efficiencies of replication origins.
2016-12-15 | GSE90939 | GEO