A5005679393- Single-cell and spatial transcriptomics
- Geological and Geophysical Studies
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Neonatal Respiratory Health Research
- Congenital heart defects research
- Cell Image Analysis Techniques
- Bioinformatics and Genomic Networks
- Neuroendocrine regulation and behavior
- Pluripotent Stem Cells Research
- Circadian rhythm and melatonin
- Advanced Proteomics Techniques and Applications
California Institute of Technology
2019-2024
Abstract Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive open-source toolbox for spatial data analysis visualization. The module provides end-to-end by implementing wide range of algorithms characterizing tissue composition, expression patterns, cellular interactions. Furthermore, single-cell RNAseq can be integrated cell-type enrichment analysis. visualization...
Abstract Molecular profiling of single cells has advanced our knowledge the molecular basis development. However, current approaches mostly rely on dissociating from tissues, thereby losing crucial spatial context regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes tissue sections mouse embryos at 8–12 somite stage. By integrating and multiplexed transcriptional...
Diverse cell types in tissues have distinct gene expression programs, chromatin states, and nuclear architectures. To correlate such multimodal information across thousands of single cells mouse brain tissue sections, we use integrated spatial genomics, imaging genomic loci along with RNAs epigenetic markers simultaneously individual cells. We reveal that type–specific association scaffolding DNA around bodies organize the architecture differential levels different types. At submegabase...
Abstract The rapid development of novel spatial transcriptomic and proteomic technologies has provided new opportunities to investigate the interactions between cells their native microenvironment. However, effective use such requires innovative computational tools that are easily accessible intuitive use. Here we present Giotto, a comprehensive, flexible, robust, open-source toolbox for data analysis visualization. module provides end-to-end by implementing wide range algorithms...
Abstract Transcriptional and epigenetic profiling of single-cells has advanced our knowledge the molecular bases gastrulation early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing crucial spatial context that is necessary for understanding cell tissue interactions during development. Here, we apply an image-based single-cell transcriptomics method, seqFISH, to simultaneously precisely detect mRNA molecules 387 selected target genes in 8-12...
Abstract Identifying the relationships between chromosome structures, chromatin states, and gene expression is an overarching goal of nuclear organization studies. Because individual cells are highly variable at all three levels, it essential to map modalities in same single cell, a task that has been difficult accomplish with existing tools. Here, we report direct super-resolution imaging over 3,660 chromosomal loci mouse embryonic stem (mESCs) by DNA seqFISH+, along 17 marks sequential...
SUMMARY At the onset of murine gastrulation, pluripotent epiblast cells migrate through primitive streak, generating mesodermal and endodermal precursors, while ectoderm arises from remaining epiblast. Together, these germ layers establish body plan, defining major axes initiating organogenesis. Although comprehensive single cell transcriptional atlases dissociated mouse embryos across embryonic stages have provided valuable insights during spatial context for differentiation tissue...
Abstract Nuclear architecture in tissues can arise from cell-type specific organization of nuclear bodies, chromatin states and chromosome structures. However, the lack genome-wide measurements to interrelate such modalities within single cells limits our overall understanding architecture. Here, we demonstrate integrated spatial genomics mouse brain cortex, imaging thousands genomic loci along with RNAs subnuclear markers simultaneously individual cells. We revealed fixed points, combined...
The seqFISH Hyb Station is a custom built platform consists ofa liquid handling pump , fluidic switcher and 96-well plate auto-sampler which aids experiments by flowing hybridization reagents washes in out of flow cell containing the biological sample. Researchers set up multi-day to perform chemistries such as hybridizations, washes, stripping. In each round hybridization, auto sampler handle will move designated well approximately 100uL readouts are flowed into made allow hybridization....