Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

ABSTRACT: Single cell atlases of platyhelminth Müller’s larva and mollusc trochophore larva reveal homologous cell types and phylum specific novelties

ORGANISM(S): Magallana gigas Prostheceraeus crozeri

PROVIDER: GSE231713 | GEO | 2023/05/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

Project description:Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

| PRJNA967338 | ENA

COVID-19 tissue atlases reveal SARS-COV-2 pathology and cellular targets

Project description:COVID-19, caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple-organ failure, but little is known about its pathophysiology. Here, we generated single-cell atlases of 23 lung, 16 kidney, 15 liver and 18 heart COVID-19 autopsy donor tissue samples, and spatial atlases of 14 lung donors. Integrated computational analysis uncovered substantial remodeling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of myofibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in COVID-19 donor heart tissue, and mapped cell types and genes implicated with disease severity based on COVID-19 GWAS. Our foundational dataset elucidates the biological impact of severe SARS-CoV-2 infection across the body a key step towards new treatments.

2021-04-09 | GSE171668 | GEO

Maximum likelihood inference of reticulate evolutionary histories.

Project description:Hybridization plays an important role in the evolution of certain groups of organisms, adaptation to their environments, and diversification of their genomes. The evolutionary histories of such groups are reticulate, and methods for reconstructing them are still in their infancy and have limited applicability. We present a maximum likelihood method for inferring reticulate evolutionary histories while accounting simultaneously for incomplete lineage sorting. Additionally, we propose methods for assessing confidence in the amount of reticulation and the topology of the inferred evolutionary history. Our method obtains accurate estimates of reticulate evolutionary histories on simulated datasets. Furthermore, our method provides support for a hypothesis of a reticulate evolutionary history inferred from a set of house mouse (Mus musculus) genomes. As evidence of hybridization in eukaryotic groups accumulates, it is essential to have methods that infer reticulate evolutionary histories. The work we present here allows for such inference and provides a significant step toward putting phylogenetic networks on par with phylogenetic trees as a model of capturing evolutionary relationships.

| S-EPMC4246314 | biostudies-literature

Ensemble learning for classifying single-cell data and projection across reference atlases

Project description:Single-cell data are being generated at an accelerating pace. How best to project data across single-cell atlases is an open problem. We developed a boosted learner that overcomes the greatest challenge with status quo classifiers: low sensitivity, especially when dealing with rare cell types. By comparing novel and published data from distinct scRNA-seq modalities that were acquired from the same tissues, we show that this approach preserves cell-type labels when mapping across diverse platforms.

2020-03-01 | GSE141982 | GEO

Evolutionary histories of breast cancer and related clones.

Project description:Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development1-3. However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more of these clones in normal tissues ultimately evolve to cancer. Here, using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, we show unique evolutionary histories of breast cancers harbouring der(1;16), a common driver alteration found in roughly 20% of breast cancers. The approximate timing of early evolutionary events was estimated from the mutation rate measured in normal epithelial cells. In der(1;16)(+) cancers, the derivative chromosome was acquired from early puberty to late adolescence, followed by the emergence of a common ancestor by the patient's early 30s, from which both cancer and non-cancer clones evolved. Replacing the pre-existing mammary epithelium in the following years, these clones occupied a large area within the premenopausal breast tissues by the time of cancer diagnosis. Evolution of multiple independent cancer founders from the non-cancer ancestors was common, contributing to intratumour heterogeneity. The number of driver events did not correlate with histology, suggesting the role of local microenvironments and/or epigenetic driver events. A similar evolutionary pattern was also observed in another case evolving from an AKT1-mutated founder. Taken together, our findings provide new insight into how breast cancer evolves.

| S-EPMC10432280 | biostudies-literature

Three-dimensional morphologic and molecular atlases of human nasal vasculatures [Human_Nasal_10X]

Project description:Three-dimensional morphologic and molecular atlases of human nasal vasculatures [Human_Nasal_10X]

| PRJNA853580 | ENA

Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia

Project description:Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia

| PRJNA1075033 | ENA

Three-dimensional morphologic and molecular atlases of human/mouse nasal vasculatures

Project description:Three-dimensional morphologic and molecular atlases of human/mouse nasal vasculatures

| PRJNA853578 | ENA

Three-dimensional morphologic and molecular atlases of murine nasal vasculatures [Mouse_Nasal_10X]

Project description:Three-dimensional morphologic and molecular atlases of murine nasal vasculatures [Mouse_Nasal_10X]