A reference cell tree will serve science better than a reference cell atlas

S Domcke, J Shendure - Cell, 2023 - cell.com
Single-cell biology is facing a crisis of sorts. Vast numbers of single-cell molecular profiles
are being generated, clustered and annotated. However, this is overwhelmingly ad hoc, and …

Connecting past and present: single-cell lineage tracing

C Chen, Y Liao, G Peng - Protein & Cell, 2022 - academic.oup.com
Central to the core principle of cell theory, depicting cells' history, state and fate is a
fundamental goal in modern biology. By leveraging clonal analysis and single-cell RNA-seq …

[HTML][HTML] Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs

S Tarazi, A Aguilera-Castrejon, C Joubran, N Ghanem… - Cell, 2022 - cell.com
In vitro cultured stem cells with distinct developmental capacities can contribute to
embryonic or extraembryonic tissues after microinjection into pre-implantation mammalian …

High-throughput total RNA sequencing in single cells using VASA-seq

F Salmen, J De Jonghe, TS Kaminski, A Alemany… - Nature …, 2022 - nature.com
Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated
transcripts, capturing only a small fraction of the total cellular transcriptome. This precludes …

Inferring and perturbing cell fate regulomes in human brain organoids

JS Fleck, SMJ Jansen, D Wollny, F Zenk, M Seimiya… - Nature, 2023 - nature.com
Self-organizing neural organoids grown from pluripotent stem cells,–combined with single-
cell genomic technologies provide opportunities to examine gene regulatory networks …

[HTML][HTML] Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution

CA Herring, RK Simmons, S Freytag, D Poppe… - Cell, 2022 - cell.com
Human brain development is underpinned by cellular and molecular reconfigurations
continuing into the third decade of life. To reveal cell dynamics orchestrating neural …

[HTML][HTML] Mouse embryo model derived exclusively from embryonic stem cells undergoes neurulation and heart development

KYC Lau, H Rubinstein, CW Gantner, R Hadas… - Cell Stem Cell, 2022 - cell.com
Several in vitro models have been developed to recapitulate mouse embryogenesis solely
from embryonic stem cells (ESCs). Despite mimicking many aspects of early development …

[HTML][HTML] A single-cell time-lapse of mouse prenatal development from gastrula to birth

C Qiu, BK Martin, IC Welsh, RM Daza, TM Le, X Huang… - Nature, 2024 - nature.com
The house mouse (Mus musculus) is an exceptional model system, combining genetic
tractability with close evolutionary affinity to humans,. Mouse gestation lasts only 3 weeks …

Primate gastrulation and early organogenesis at single-cell resolution

J Zhai, J Guo, H Wan, L Qi, L Liu, Z Xiao, L Yan… - Nature, 2022 - nature.com
Our understanding of human early development is severely hampered by limited access to
embryonic tissues. Due to their close evolutionary relationship with humans, nonhuman …

Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development

L Fei, H Chen, L Ma, WE, R Wang, X Fang, Z Zhou… - Nature Genetics, 2022 - nature.com
Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell
differentiation. Recent advances in single-cell genomics are altering our understanding of …