10x Genomics Blog

Researchers from 39 institutes and hospitals across China have come together to deeply profile the immune response to SARS-CoV-2 infection. A testament to the potential of scientific collaboration in enabling large-cohort studies, they collectively performed single cell RNA-sequencing on 284 samples from 196 COVID-19 patients and controls, totaling 1.46 million cells. 

Explore their findings regarding the influence of population demographics on the immune landscape, surprising evidence of immune cell susceptibility to SARS-CoV-2 infection, and new cellular culprits of the cytokine storm. Plus, find out how 10x Genomics scientists played a part in enabling the success of this team effort, from connecting labs in the midst of a global pandemic to providing guidance and reagents.

April is Irritable Bowel Syndrome (IBS) Awareness Month, and chances are you know someone who struggles with this common disorder. Though it’s estimated that 10–15% of the population has IBS—or between 25 and 45 million people in the United States—it is commonly undiagnosed (1). Worse, the exact cause of IBS remains unknown, and while treatments do exist, they may not completely address symptoms.

Inflammatory bowel disease (IBD), which is diagnosed by the presence of inflammation in the gut, is an umbrella term that encompasses Crohn’s disease, ulcerative colitis, and other syndromes, like IBS. Because IBD and IBS are believed to involve the gut–brain axis, and this enteric nervous system has not yet been well characterized, single cell tools will help enable a deeper understanding of both the heterogeneity of this “second brain” and its complexity, or, how these cells interact with surrounding endothelial, stromal, and immune cells. In this post, we take a look at one research paper that uses single cell sequencing to build an atlas of the human and mouse colon in an effort to understand the disease mechanism behind IBD—and how this knowledge might inform the development of improved therapies.

While the field of single cell biology has seen the power of what single cell gene expression analysis can do, researchers are increasingly pairing spatial location with transcriptomics to make even further strides in the areas of immunology, cancer, neuroscience, and others. In this feature, we’ll spotlight the work of one scientist, Dr. Roser Vento-Tormo at the Wellcome Sanger Institute, who is using single cell and spatial tools to advance our understanding of the interaction between maternal and fetal cells in the womb. Read more to find out how these paired insights into cell–cell interactions are poised to advance women’s health.

102. That’s how many risk genes have been associated with autism spectrum disorder, according to one study (ASD; 1). This number may not seem very large but consider that there are some disorders with only a single gene involved, like cystic fibrosis and sickle cell anemia (2). 

March is National Autoimmune Disease Awareness Month, and for the millions of people who suffer from a disease with no cure, education is key to advances in research and therapies. In this blog post, we highlight two publications that use single cell tools to study the origins of multiple sclerosis and Crohn’s disease. Both studies were launched with the aim of learning more about how these diseases develop by comparing single cell states in disease to healthy immune system surveillance and normal embryonic development, respectively. Our hope is to promote not only awareness of autoimmunity-related diseases but also showcase the higher potential of applying 10x Genomics single cell and spatial solutions to impact human health.

If you had all the time and resources in the world, what might you discover? That’s not a question any researcher could answer, but it’s a powerful idea, and something that has driven a great deal of scientific progress. Scientists are problem solvers, trained to overcome challenges and limitations—developing new methods to meet their needs, or devising alternative research angles for widely studied topics like cancer. Their tools should be reliable and efficient problem solvers, too. 

Patricia Rogers, Associate Director of the Flow Cytometry Core Lab at the Broad Institute, has always approached instrumentation with the needs of a core lab in mind. Made up of six scientists, four of whom focus on flow cytometry, the lab’s decision to branch out into genomics services was straightforward—they wanted to provide researchers with a more complete service. However, deciding on the types of instrumentation to bring in was less so. The team members at the Flow Core Lab work with a wide variety of sample types from both mouse and human tissues and whole blood, helping researchers studying a wide range of diseases, including cancer, diabetes, psychiatric disorders, and more. For a facility that caters to a substantial community of researchers whose projects range in topic, scale, and method, choosing a new tool can be a complicated decision.

Complex molecular circuits enable cancer cells to resist the effects of immune checkpoint inhibitors (ICIs), molecules intended to unleash T cells to destroy cancer. To tease out the details of these evasion tactics, scientists are turning to multimodal single cell CRISPR screens, which enable functional characterization of participating regulatory drivers and their molecular pathways at scale, to investigate previously hidden mechanisms of evasion that may pose novel therapeutic targets. Learn about recent advances in this field with two studies out of the New York Genome Center, NYU, and the Broad Institute of MIT and Harvard. 

Have you heard the news? Back in January, Nature Methods announced spatially resolved transcriptomics was its 2020 Method of the Year, and we were absolutely thrilled. Judging by the responses to their Twitter announcement, we weren’t the only ones.  

The increasing number of preprints and publications featuring spatial transcriptomics highlights the growing popularity and utility of spatial profiling methodologies. In fact, at the time of writing this blog, a search of the bioRxiv preprint archive for the term “spatial transcriptomics” yielded 480 results, 70 of which were submitted in 2021. 

After facing significant setbacks in Alzheimer’s disease (AD) drug development (1), many scientists are going back to basics and aiming for a more fundamental understanding of disease mechanisms, keen to discover early changes at the level of individual cells. 

At the 10x Genomics Global Cell Therapy Virtual Symposium, held February 8–12, leading cancer immunotherapy researchers discussed the challenges and promises of T-cell therapy. In this post, we highlight key points of the panel roundtable, including discussion points around four key themes: characterizing the leukapheresis and infusion product, the evolution of the cell product in vivo, mechanisms of resistance, and next-generation cell therapies.