How can you ensure that your single cell RNA sequencing (scRNA-seq) studies have the best chance of success? As with so...
Spatial transcriptomics is transforming cancer research by enabling detailed analysis of tumor complexity while preserving natural cell interactions. This innovative technique allows researchers to visualize gene expression patterns within the tumor microenvironment, uncovering interactions between different cell types and surrounding structures such as blood vessels and immune cells. By integrating spatial transcriptomics with advanced computational tools, scientists can identify biomarkers, map signaling pathways, and understand how these factors influence treatment response and resistance. This approach holds great promise for advancing personalized medicine in oncology, facilitating the development of targeted therapies tailored to individual patients based on their unique tumor biology.
The Innovator Blog Series celebrates research conducted by 10x Genomics customers who have demonstrated scientific ingen...
The advent of single cell assays, such as 3'GEX and 5'GEX, has revolutionized our research in various fields like oncology, developmental biology, and immunology by enabling detailed gene expression analysis at a single-cell resolution. However, their reliance on fresh samples limited their application. Chromium Fixed RNA profiling- a highly sensitive probe-based technology- overcomes these challenges by allowing sample preservation and transport without the quality losses, simplifying logistics. It enhances efficiency by enabling sample batching and multiplexing. The technology also barcodes up to 1 million cells in 6 minutes, reducing hands-on time and errors. Additionally, its compatibility with FFPE tissues and integration with Visium and Xenium spatial solutions provides comprehensive disease insights, pushing the boundaries of innovation in research and beyond.
Alex Rolland and his team at Cancer Treatment Options and Management Inc. focus on advancing oncology research to enhance cancer diagnostics and treatment effectiveness. Their collaboration with Norgen Biotek has yielded significant advancements in liquid biopsy technology, particularly in extracting circulating tumor DNA (ct-DNA) and exosomal RNA from patient blood samples. By utilizing Norgen's innovative extraction kits, they achieved high yields of cancer-specific ct-DNA fragments, crucial for monitoring treatment responses and disease progression. Their approach includes custom probes to monitor treatment responses and detect mutations, crucial for guiding personalized therapies and improving patient outcomes worldwide.
The impressive capabilities of the 10x Genomics 5,000-plex human gene expression panel were demonstrated using the Xenium Analyzer system, which successfully imaged a total area of 420 mm² over 124 hours. A deep analysis of a human liver sample slide revealed an average of 408 transcripts per cell across 1,018,026 cells, with a low false discovery rate of just 0.3%. This detailed examination identified 26 distinct cell types and five unique spatial niches, confirmed by visualizing marker genes for accurate cell type and neighborhood assignments. The 5,000-plex panel offers comprehensive coverage, making it an excellent tool for classifying cell types, exploring drug target interactions, investigating cell-cell signaling, and mapping biological pathways across all human tissues.
Those limitations are why our team developed this single cell RNA sequencing (scRNA-seq) protocol for PFA-fixed tissues. In this blog you’ll get a quick snapshot of how it offers you access to more samples, lets you process them on your schedule, retains your sample quality throughout storage and transport, and provides the greatest sensitivity of any commercial fixed RNA profiling protocol. Or, if you’re ready to jump right in, we have a direct link to the protocol and a webinar that goes into greater depth (and also offers a preview of FFPE tissue compatibility).
With Visium's high-resolution spatial capture technology and intuitive software, researchers can visualize gene and protein expression like never before. From understanding cellular dynamics to deciphering disease mechanisms, Visium empowers researchers across diverse fields to embark on a journey of discovery, uncovering the secrets of tissue biology and disease pathology with style and precision.
Understanding tumor invasiveness is challenging due to subtle heterogeneity. The Xenium In Situ platform from 10x Genomics integrates single-cell resolution with spatial gene expression to uncover detailed heterogeneity in tumors. In a breast cancer study, it identified a rare triple-positive region (HER2+/ER+/PR+), crucial for prognosis and treatment. Xenium uses high-sensitivity padlock probes to create a spatial map of transcripts at subcellular resolution and preserves tissue for further analysis. This powerful tool enhances cancer research by providing comprehensive molecular insights and improving diagnostic and treatment strategies.
Spatial transcriptomics, a revolutionary technique that unveils gene activity within tissues, is transforming biological research. 10x Genomics offers two powerful solutions, Visium HD and Xenium In Situ, that provide a more holistic view of gene expression. Visium HD analyzes the entire transcriptome across large areas, making it ideal for initial discovery. Xenium In Situ, on the other hand, focuses on a targeted set of genes with exceptional resolution, perfect for validating prior findings. By using these complementary methods together, researchers can unlock a deeper understanding of gene expression within tissues.
Spatially transcriptomics is crucial for understanding how cell location influences gene expression, development, and disease. This field has evolved from early techniques like radioactive in situ hybridization to advanced methods such as sequencing-based Visium Spatial and imaging-based Xenium In Situ. These technologies allow researchers to analyze gene expression within the natural cellular context, revealing new biological insights across various fields, including developmental biology, cancer, and neuroscience. Choosing the right method depends on research goals, with sequencing-based methods suited for hypothesis generation and imaging-based methods for detailed hypothesis testing and specific target analysis.
Cancer is a multifaceted disease driven by the complex interplay of diverse immune cells. To elucidate the heterogeneity of tumor microenvironments and assess the efficacy of innovative therapeutics, leveraging Chromium Single Cell Multiome ATAC + Gene Expression for comprehensive epigenetic profiling is essential. This advanced technique is pivotal in deciphering the mechanisms of gene activation and silencing that propel cancer progression.
