10x Genomics Blog

Find answers to your questions about the latest addition to our Visium Spatial Platform: Visium Spatial Gene Expression with Immunofluorescence. Gain a new perspective on tissue complexity with the ability to visualize histology, whole transcriptome gene expression, and protein expression in the same tissue section.

Complex, heterogeneous tissues are made up of multiple cell types and states, and, while deciphering that information is essential, it’s the tip of the iceberg. To fully characterize your tissue sample, you need an approach that allows you to analyze a single sample from multiple perspectives, providing a more complete understanding of the relationships between tissue architecture and cellular phenotype and function. Visium Spatial Gene Expression with Immunofluorescence combines the strengths of spatial transcriptomic and immunofluorescence (IF) capabilities to create a multianalyte spatial approach to whole tissue analysis, providing whole transcriptome gene expression data with protein detection while maintaining morphological context.

Index hopping occurs when reads from an RNA-seq library are assigned to the wrong sample. Though it’s usually a rare phenomenon, index hopping can introduce deleterious artifacts into single cell RNA-seq experiments. Now, with dual indexing for all 10x Genomics transcriptomic libraries, you can approach your single cell and spatial experiments with greater confidence. Read on to explore dual indexing and how it mitigates these sequencing challenges, and learn more in our Technical Note.

We know index hopping can negatively impact sequencing data, but where does it come from? How does index hopping happen, and how do sequencers unintentionally enable it?

We recently announced the launch of our new Targeted Gene Expression Solution. Find out how targeted gene expression can help you increase the scale of your experiments while decreasing sequencing costs, and explore a use case for single cell CRISPR screens, published by a team of scientists from UCSF.

Capturing a part of the whole: why target enrichment?

The discovery power of single cell and spatial whole transcriptome analysis is well known. Given a complex mixture of cells, or a thinly sliced tissue sample, scientists can profile total mRNA expression from individual or small clusters of cells, deriving meaningful conclusions about cell identities, functional states, and local cellular relationships and interactions, all without the need for pre-selection of known marker genes. The tested value of this analytical method is balanced, however, by the everyday realities of the research process. From the largest institutions and biotech companies to individual laboratories and projects, researchers are trying to push the boundaries of biological discovery and explore their scientific passions while optimizing their experiments with the resources they have.

Achieve comprehensive tissue phenotyping with spatially resolved whole transcriptome and immunofluorescence protein co-detection. Learn more about our new protocol, Visium Spatial Gene Expression with Immunofluorescence, in this upcoming webinar.

Beyond the transcriptome: Why single cell epigenomics?

Long have researchers searched the transcriptome for biological insights into complex cell populations and processes. Innate sample heterogeneity and cell-to-cell differences in gene expression required that scientists move beyond averaged bulk measurements to single cell RNA-sequencing in order to develop a more accurate picture of complex biological systems. However, the transcriptome may not tell a cell's entire story, and scientists often want to understand the how establishing the what—that is, the mechanistic explanation for the changing patterns of gene expression they observe through transcriptional profiling.

Recently, we held our Single Cell Epigenomics Scientific Challenge, where researchers submitted proposals for a single cell chromatin accessibility experiment. Now, we congratulate our three winners: Linda Smit, PhD, of VUmc Cancer Center Amsterdam, Carolina Soriano-Tarraga, PhD, of Washington University in St. Louis, and Koji Taniguchi, MD, PhD, of Keio University School of Medicine. From the mechanisms of cancer therapy resistance to the drivers of Alzheimer’s disease to the basis of inflammatory memory, find out what epigenetic insights they plan to uncover with the Chromium Single Cell ATAC Solution.

Today, we come together to celebrate a momentous accomplishment: 1,000 peer-reviewed publications leveraging 10x Genomics technology. We’d like to thank and congratulate the many graduate students, postdocs, PIs, laboratory technicians, bioinformaticians, and institutions who have taken up the call to resolve complex biology in order to advance human health.

Hear from Katie Sullivan-Bibee, Senior Supervisor of Molecular Biology Assay Development at 10x Genomics, as she shares her story of coming to love science and nature. Plus, find resources to raise your own little scientists with an appreciation for scientific exploration and discovery.

Growing up in the Bay Area, Katie Sullivan-Bibee, Senior Supervisor of Molecular Biology Assay Development at 10x Genomics, was always fascinated by animals and nature as a child. She attributed her passion for scientific exploration today to some of her earliest experiences interacting with the natural world:

Find support for your single cell and spatial experiments during laboratory shutdowns. Explore resources from the 10x Genomics Technical Support Team, addressing how to store samples, when to safely pause your experiments, and more.

Many individuals and organizations have been significantly impacted by the coronavirus and subsequent public health ordinances to shelter in place. Scientists and research institutions are among those who continue to face challenges as a result of a number of laboratory shutdowns, including unfortunate loss of animal cohorts, cell lines, and, critically, time.

Researchers around the world are responding to the need to understand the underlying biology of the novel coronavirus. They are studying how the virus infects, what determines cell type-specific susceptibility to infection, what degree of immune response distinguishes severe and mild cases, and what antibodies can be leveraged to target and stop the virus.