10x Genomics Blog

  • Unlocking lung tumor heterogeneity: single cell analysis reveals a high-plasticity cell state

    Jeanene Swanson on November 30, 2020

    While there are numerous treatment options for lung cancer, it remains a notoriously difficult cancer to treat if not caught early since most lung tumors eventually become resistant to chemotherapy, a mainstay treatment. For Lung Cancer Awareness Month, we feature recent research that underscores the potential of single cell techniques to uncover drivers of tumor progression and treatment resistance. In this work, scientists discovered a new, highly plastic cell state that they believe plays a large role in tumors becoming resistant to chemotherapy. Read more to learn how single cell transcriptome profiling and chromatin accessibility mapping is allowing scientists to discern surprising insights into tumor evolution.

    Kras-Driven Lung Cancer. Created by Eric Snyder, 2015. CREDIT: National Cancer Institute on Unsplash.
    Kras-Driven Lung Cancer. Created by Eric Snyder, 2015. CREDIT: National Cancer Institute on Unsplash.
  • The case of the missing T cells: why integrated multimodal data holds the key

    Olivia Habern on November 24, 2020

    “We want to be able to move beyond a descriptive analysis. We want to move beyond just saying, how many cell types do we have in our sample? And instead, we want to start to identify the key transcription factors and genetic regulators that influence the system. And that's what paired RNA and ATAC-seq data can help us start to do.”

    Dr. Rahul Satija, Core Faculty Member, New York Genome Center

    Dr. Rahul Satija, head of the Satija Lab and Core Faculty Member at the New York Genome Center, shared these insights in a recent webinar introducing the capabilities of Seurat v4, the latest version of his lab's R toolkit for the analysis and integration of single cell datasets. Review his talk to learn how integrating multimodal single cell datasets, including gene expression and chromatin accessibility data, can unmask not only previously hidden cellular heterogeneity in your samples, but also key epigenetic regulators of cellular identity and function.

  • Kicking off the Clinical Translational Research Network: research stories from the roundtable

    Liz Lucero on November 23, 2020

    Researchers from around the world came together virtually for our inaugural Clinical Translational Research Network (CTRN) roundtable meeting earlier this month. The CTRN program fosters communication and collaboration among leading researchers who are working to bridge the gap between bench and bedside. Explore their insights into how the integration of single cell and spatial tools can advance clinical translational research for cancer, tissue fibrosis, and more.

  • Deciphering the complex biology of neurodegenerative diseases: looking back at the Global Neuroscience Virtual Symposium

    Liz Lucero on November 20, 2020

    Around the world, neuroscientists are working to understand the fundamental biology underlying debilitating neurological diseases. At our recent Global Neuroscience Virtual Symposium, we heard from leading researchers pushing the boundaries and creating new inroads into the study of neurodegenerative disease.

    Credit: Jonathan Bailey, NHGRI.
    Credit: Jonathan Bailey, NHGRI.
  • Introducing Visium Gateway: your entry to the world of spatial gene expression

    Leidamarie Tirado-Lee on November 19, 2020

    Spatial gene expression profiling allows you to see your tissues in a whole new way with a comprehensive view of the spatial organization of newly discovered cell types, states, and biomarkers. Read this blog post to learn about the power of Visium Spatial Gene Expression and our new Visium Gateway slides.

    A picture is worth a thousand words. Imagine where biology would be if microscopes had not existed to allow Robert Hooke to discover cellular structures in cork (1). Where would medicine be without Rudolph Virchow’s observations that cellular changes are at the root of all disease (2), giving birth to the field of cellular pathology? Undoubtedly, the ability to view cells and the tissues they make up with microscopes revolutionized science and medicine.

  • Single cell techniques enable progress in making islet transplantation a reality for more people with diabetes

    Jeanene Swanson on November 18, 2020

    In honor of National Diabetes Awareness Month, we highlight a promising development in treatment options for patients with type 1 diabetes. Beyond drugs that manage the symptoms of diabetes, patients may consider pancreatic islet transplantation as an experimental treatment to restore crucial insulin-secreting beta cells, but transplants can be rejected by the body and donors are limited. Now, with the help of single cell analysis, scientists have discovered a key signaling pathway that induces successful differentiation of stem cells into functional beta-like cells, expanding the options for patients with diabetes.

    The pancreas has a role in digestion, highlighted here. Ducts in the pancreas (green) conduct digestive enzymes into the duodenum. This image also shows a pancreatic islet, part of the endocrine pancreas, which contains cells responsible for secretion of insulin and glucagon. CREDIT: Illustration from Anatomy & Physiology, Connexions Website. http://cnx.org/content/col11496/1.6/ (2013). (CC BY 3.0)
    The pancreas has a role in digestion, highlighted here. Ducts in the pancreas (green) conduct digestive enzymes into the duodenum. This image also shows a pancreatic islet, part of the endocrine pancreas, which contains cells responsible for secretion of insulin and glucagon. CREDIT: Illustration from Anatomy & Physiology, Connexions Website. http://cnx.org/content/col11496/1.6/ (2013). (CC BY 3.0)
  • A data tale: finding the story in your single cell gene expression data

    Olivia Habern on November 12, 2020

    We spoke with Eleanor Howe, PhD, Founder and CEO of Diamond Age Data Science, a Compatible Product Partner with 10x Genomics, to get her take on the best approaches to single cell gene expression experimental design and data analysis. Read on to learn how making connections as part of her research expanded her career and find expert tips and tools for single cell RNA-seq analysis to help you unlock the story of your data.

     t-SNE plot of 7,859 cells from a dissociated human melanoma sample. Each cell is represented by a single dot. Broad categories of immune cell populations were identified through gene expression signatures. CREDIT: 10x Genomics. LIT000089 Rev B Multiomic profiling of the immune system.
    t-SNE plot of 7,859 cells from a dissociated human melanoma sample. Each cell is represented by a single dot. Broad categories of immune cell populations were identified through gene expression signatures. CREDIT: 10x Genomics. LIT000089 Rev B Multiomic profiling of the immune system.
  • Investigating the plaque microenvironment in Alzheimer’s disease with spatial gene expression

    Jeanene Swanson on November 6, 2020

    Extracellular amyloid beta, intracellular tau protein deposits, and neuronal loss represent the classical hallmarks of Alzheimer’s disease. However, scientists are well aware that pathways involving non-neuronal brain cells are also dysregulated throughout the course of disease and likely play an important role in disease pathogenesis. In a recent study, scientists leveraged spatial gene expression approaches to study the molecular pathology of this degenerative brain disease, revealing key molecular changes and cellular interactions within a network of glial cells in the vicinity of amyloid plaques. Read more to learn how spatial analysis is opening up new insights into the cellular contribution of glia to inflammation and overall disease progression in AD.

    Beta-Amyloid Plaques and Tau tangles in the Brain. In the Alzheimer’s affected brain, abnormal levels of the beta-amyloid protein clump together to form plaques (seen in brown) that collect between neurons and disrupt cell function. Abnormal collections of the tau protein accumulate and form tangles (seen in blue) within neurons, harming synaptic communication between nerve cells. CREDIT: National Institute on Aging, NIH.
    Beta-Amyloid Plaques and Tau tangles in the Brain. In the Alzheimer’s affected brain, abnormal levels of the beta-amyloid protein clump together to form plaques (seen in brown) that collect between neurons and disrupt cell function. Abnormal collections of the tau protein accumulate and form tangles (seen in blue) within neurons, harming synaptic communication between nerve cells. CREDIT: National Institute on Aging, NIH.
  • Strengthening the core: collaboration when tissue meets genomics at Newcastle University

    Olivia Habern on October 29, 2020

    What do pathologists and tissue microscopy experts say to genomics experts and bioinformaticians? At Newcastle University, they say, “Hey, let’s work together.” As genomic approaches become staples of biological research, scientific partnerships like these will help power new discoveries. For scientists at Newcastle, collaboration was forged by each group’s common ties to Visium Spatial Gene Expression, a solution offered by 10x Genomics that enables unbiased characterization of spatially resolved whole transcriptome gene expression in thousands of spots across a section of tissue on a tissue slide.

    Visium Spatial Gene Expression Slides, stained and unstained.
    Visium Spatial Gene Expression Slides, stained and unstained.