10x Genomics Blog

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.

Expand your traditional tissue gene expression assays by combining Visium Spatial Solutions with our new Targeted Gene Expression panels. Scale up from a few genes of interest to all relevant genes and pathways by combining high-throughput spatial gene expression with the efficiency of targeted panels.

Leveraging single cell sequencing, scientists recently discovered that neural interleukin 17a signaling driven by meningeal γδ17 T cells is correlated with anxiety-like behavior in mice. This finding uncovers new insights into complex neuroimmune interactions, and points to immune signaling molecules as possible therapeutic targets for anxiety disorders. Explore further applications of single cell and spatial technology to the study of complex neuropsychiatric disorders and neurodegenerative diseases at our upcoming Global Neuroscience Virtual Symposium.

October is National Breast Cancer Awareness Month in the United States. To help raise awareness, we wanted to profile recent publications that highlight current advances in research toward targeted breast cancer therapies, including studies of HER2-positive and triple negative breast cancers. With the insights provided by single cell RNA-sequencing into the cellular heterogeneity of both tumors and the tumor microenvironment (TME), researchers are gaining a more detailed understanding of why standard-of-care therapies may not be effective for some cancers, how more than one therapy can be combined to improve treatment outcomes, and how certain cells can be pinpointed as therapeutic targets.

Find answers to your pressing questions about the new single cell multiomics solution from 10x Genomics: Chromium Single Cell Multiome ATAC + Gene Expression. From nuclei isolation protocols to multiomic data analysis and integration, dive deeper into the experimental considerations for simultaneously profiling gene expression and open chromatin from the same cell, and explore the discovery power of a truly dual assay.

Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease without a cure. Dr. Naftali Kaminski, Professor of Medicine (Pulmonary) at Yale School of Medicine, is one of the trailblazers that has been advancing our understanding of the molecular and cellular basis of the disease. Using single cell sequencing, his laboratory has built an IPF Cell Atlas that is helping define disease-specific transcriptional profiles and functions in disease pathophysiology.

September is National Childhood Cancer Awareness Month in the United States. To help raise awareness, we wanted to take this opportunity to dig into some of the latest research on pediatric cancers, including recent studies of pediatric ependymoma, a cancer that affects the brain and spinal cord, and B cell acute lymphoblastic leukemia (B-ALL). With the insights provided by single cell RNA-sequencing into tumor heterogeneity and the cellular composition of the tumor microenvironment, researchers are gaining more comprehensive knowledge of the ‘ins and outs’ of childhood cancer as they search for better therapies.

Dr. Julie Siegenthaler, Associate Professor in the Department of Pediatrics, Section of Development Biology, at the University of Colorado, has studied the meninges for years. Now, she is filling a knowledge gap in the neuroscience community’s understanding of embryonic meningeal fibroblast heterogeneity, development, and function, with the help of single cell RNA-sequencing. These findings have the potential to illuminate the role of central nervous system (CNS) vasculature on the development of the embryonic brain and crucial protective structures like the blood-cerebrospinal fluid barrier.

When it comes to understanding central nervous system (CNS) development, health, and disease, researchers need to think outside of the box. Sometimes that leads them to structures outside of the brain. The meninges are composed of three membrane layers, including the dura, arachnoid, and pial layers, which encase the CNS from the earliest stages of embryonic development and serve as a protective covering later in adulthood. These layers contain various cell types, including meningeal fibroblasts and immune cells, and are integrated with a network of blood and lymphatic vessels that deliver oxygen, nutrients, and developmental signals to the CNS.

ATAC plus gene expression, together at last

Single cell gene expression has revolutionized how we think about biology, and cellular heterogeneity in particular. Rather than accepting an average snapshot of how cells work, scientists now have the ability to tease apart how seemingly homogenous cell lines can respond differently to the same agonist or how a defect in a rare cell type, that would otherwise be masked by its neighbors, can contribute to disease.

Despite how much positive press the transcriptome gets, however, it is ultimately the byproduct of a highly coordinated program of gene expression regulated by the epigenome. The epigenome is informed by your DNA’s chromatin state, which can be open (and accessible) or closed (and inaccessible). Chromatin state impacts how DNA-binding proteins like transcription factors or RNA polymerase can interact with genomic DNA, meaning that epigenomic regulation not only informs developmental decisions, disease progression, and therapeutic response, but also often precedes transcriptional changes and can be used to unravel otherwise indistinguishable cell types.

The failure of many clinical trial drug candidates for Alzheimer’s Disease targeting amyloid-beta plaques is renewing efforts to study brain cells at a more fundamental level. Here we highlight recent publications that use single cell RNA-seq as a valuable tool in basic research for high resolution characterization of non-neuronal cells in AD and preclinical assessment of a therapeutic candidate.