A5013939484- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Pluripotent Stem Cells Research
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Neurogenesis and neuroplasticity mechanisms
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Immune cells in cancer
- MicroRNA in disease regulation
- Neuroinflammation and Neurodegeneration Mechanisms
- Cell Image Analysis Techniques
- Liver physiology and pathology
- Extracellular vesicles in disease
- Cancer-related molecular mechanisms research
- Photoreceptor and optogenetics research
- Liver Disease Diagnosis and Treatment
- Microfluidic and Bio-sensing Technologies
- Gene Regulatory Network Analysis
- T-cell and B-cell Immunology
- Genetics, Aging, and Longevity in Model Organisms
- SARS-CoV-2 and COVID-19 Research
- Nuclear Structure and Function
- Autophagy in Disease and Therapy
BGI Research
2024-2025
BGI Group (China)
2021-2025
Shenzhen Pingle Orthopedic Hospital
2025
University of Michigan
2024
Shanxi Medical University
2024
Chinese Academy of Sciences
2018-2023
Guangzhou Institutes of Biomedicine and Health
2018-2023
Zhejiang Lab
2023
University of Chinese Academy of Sciences
2018-2020
Guangzhou Regenerative Medicine and Health Guangdong Laboratory
2019-2020
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view current methodologies precludes their systematic application analyze relatively large three-dimensional mid- late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays in situ RNA capture create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied...
Abstract Tissue regeneration requires coordination between resident stem cells and local niche 1,2 . Here we identify that senescent are integral components of the skeletal muscle regenerative repress at all stages life. The technical limitation senescent-cell scarcity 3 was overcome by combining single-cell transcriptomics a enrichment sorting protocol. We identified isolated different cell types from damaged muscles young old mice. Deeper transcriptome, chromatin pathway analyses revealed...
The molecular mechanism underlying brain regeneration in vertebrates remains elusive. We performed spatial enhanced resolution omics sequencing (Stereo-seq) to capture spatially resolved single-cell transcriptomes of axolotl telencephalon sections during development and regeneration. Annotated cell types exhibited distinct distribution, features, functions. identified an injury-induced ependymoglial cluster at the wound site as a progenitor population for potential replenishment lost...
Abstract Muscle atrophy and functional decline (sarcopenia) are common manifestations of frailty critical contributors to morbidity mortality in older people 1 . Deciphering the molecular mechanisms underlying sarcopenia has major implications for understanding human ageing 2 Yet, progress been slow, partly due difficulties characterizing skeletal muscle niche heterogeneity (whereby myofibres most abundant) obtaining well-characterized samples 3,4 Here we generate a...
Quantifying spatiotemporal dynamics during embryogenesis is crucial for understanding congenital diseases. We developed Spateo (https://github.com/aristoteleo/spateo-release), a 3D modeling framework, and applied it to mouse atlas at E9.5 E11.5, capturing eight million cells. enables scalable, partial, non-rigid alignment, multi-slice refinement, mesh correction create molecular holograms of whole embryos. It introduces digitization methods uncover multi-level biology from subcellular organ,...
Abstract Single-cell technologies are becoming increasingly widespread and have been revolutionizing our understanding of cell identity, state, diversity function. However, current platforms can be slow to apply large-scale studies resource-limited clinical arenas due a variety reasons including cost, infrastructure, sample quality requirements. Here we report DNBelab C4 (C4), negative pressure orchestrated, portable cost-effective device that enables high-throughput single-cell...
Cells do not live in a vacuum, but milieu defined by cell–cell communication that can be measured via emerging high-resolution spatial transcriptomics approaches. However, analytical tools fully leverage such data for kinetic modeling remain lacking. Here we present Spateo ( aristoteleo/spateo-release ), general framework quantitative spatiotemporal of single-cell resolution transcriptomics. delivers novel methods digitizing layers/columns to identify spatially-polar genes, and develops...
Abstract Single cell approaches have increased our knowledge about the type composition of non-human primate (NHP), but a detailed characterization area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data 358,237 cells from prefrontal cortex (PFC), primary motor (M1) visual (V1) adult female cynomolgus monkey brain, integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing)...
Abstract In contrast to rodents, the mechanisms underlying human trophectoderm and early placenta specification are understudied due ethical barriers scarcity of embryos. Recent reports have shown that pluripotent stem cells (PSCs) can differentiate into (TE)-like (TELCs) trophoblast (TSCs), offering a valuable in vitro model study specification. Here, we demonstrate VGLL1 (vestigial-like family member 1), which is highly expressed during non-human primate TE vivo but negligibly mouse,...
Abstract Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate the factor Sox2 is able directly RNA in vitro well mouse and human cells. targets via a 60-amino-acid binding motif (RBM) positioned C-terminally of high mobility group (HMG) box. can associate with simultaneously form ternary RNA/Sox2/DNA complexes. Deletion RBM does not affect selection target genes but mitigates pluripotency related...
The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles mouse reprogramming. On one side, induces pro-senescence factor Ink4a degrades pluripotency regulator PHF20 a factor-independent manner. other specifically recruited by to reduce H3K27me3 at both enhancers...
The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, genetic-related variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons revealing cell type-specific...
SUMMARY High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study brain aging. Here, we introduce transcriptomic and chromatin accessibility landscape 1,985,317 cells from eight regions 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up 29-years old. This dataset uncovers dynamic molecular changes in critical functions such as synaptic communication axon myelination, exhibiting high degree cell type...
ABSTRACT Stopping COVID-19 is a priority worldwide. Understanding which cell types are targeted by SARS-CoV-2 virus, whether interspecies differences exist, and how variations in state influence viral entry fundamental for accelerating therapeutic preventative approaches. In this endeavor, we profiled the transcriptome of nine tissues from Macaca fascicularis monkey at single-cell resolution. The distribution facilitators, ACE2 TMRPSS2, different subtypes showed substantial heterogeneity...
Teratoma, due to its remarkable ability differentiate into multiple cell lineages, is a valuable model for studying human embryonic development. The similarity of the gene expression and chromatin accessibility patterns in these cells those observed vivo further underscores potential as research tool. Notably, teratomas derived from naïve (pre-implantation epiblast-like) pluripotent stem (PSCs) have larger diversity contain extraembryonic making them more suitable study developmental...
SUMMARY Spatially resolved transcriptomic technologies are promising tools to study cell fate decisions in a physical microenvironment, which is fundamental for enhancing our knowledge of mammalian development. However, the imbalance between resolution, transcript capture and field view current methodologies precludes their systematic application analyze relatively large three-dimensional mid- late-gestation embryos. Here, we combined DNA nanoball (DNB) patterned arrays tissue RNA create...