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Search · four archives
15 papers · ranked by Valyu relevance
Lizhi He, Bin Wang, Timothy Wiggin, Renchao Chen + 18 more
Spatial transcriptomics has emerged as a transformative approach for elucidating tissue architecture, cellular heterogeneity, and disease mechanisms by preserving the spatial context of gene expression in cells. Despite these advances, many spatial transcriptomic methods underperform in archival or clinically relevant…
Xinbin Tang, Jiayu Chen, Xinya Zhang, Xuzhu Liu + 6 more
Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression. In situ sequencing (ISS) is a targeted spatial transcriptomic technique that is based on padlock…
Ebtesam A. Abdel-Shafy, Moussa Kassim, Alessia Vignoli, Farag Mamdouh + 17 more
Spatial transcriptomics provides researchers with a powerful tool to investigate gene expression patterns within their native positional context in tissues, revealing intricate cellular relationships. However, analyzing spatial transcriptomics data presents unique challenges due to their high dimensionality and…
Archibald Enninful, Zhaojun Zhang, Dmytro Klymyshyn, Hailing Zong + 12 more
Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics…
Sergio Marco Salas, Paulo Czarnewski, Louis B. Kuemmerle, Saga Helgadottir + 12 more
The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10X Genomics capable of mapping hundreds of transcripts in situ at a subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis…
Cecilia Cisar, Nicholas Keener, Mathew Ruffalo, Benedict Paten
In recent years, high-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and the effects it may have on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own…
Kyle A. Vanderschoot, Jacob P. Padilla, Kelli A. Steineman, Christopher M. De Caro + 2 more
Current spatial gene expression methods use DNA microarrays, Next Generation Sequencing (NGS), and fluorescence microscopy to depict the pathological/histological architecture of tissues. While each of these techniques has its own advantages, they are often costly, time intensive, and limit sampling area. A newly…
Lars E. Borm, Alejandro Mossi Albiach, Camiel C.A. Mannens, Jokubas Janusauskas + 6 more
Methods to spatially profile the transcriptome are dominated by a trade-off between resolution and throughput. Here, we developed a method named EEL FISH that can rapidly process large tissue samples without compromising spatial resolution. By electrophoretically transferring RNA from a tissue section onto a capture…
Aditya Venkatramani, Didar Ciftci, Limor Cohen, Christopher Li + 2 more
Spatial omics has brought a fundamental change in the way that we study cell and tissue biology in health and disease. Among various spatial omics methods, genome-scale imaging allows transcriptomic, 3D-genomic, and epigenomic profiling of individual cells with high spatial (subcellular) resolution but often requires a…
Xun Ding, Kendall Hoff, Radha Swaminathan, Mikaela Koutrouli + 13 more
Spatial transcriptomics enables analysis of gene expression that is spatially resolved within a tissue section, making it possible to elucidate the relationship between individual cells within the context of the tissue. This transformative technology enables researchers to better understand gene function within the…
Joshua A. Weinstein, Aviv Regev, Feng Zhang
Analyzing the spatial organization of molecules in cells and tissues is a cornerstone of biological research and clinical practice. However, despite enormous progress in profiling the molecular constituents of cells, spatially mapping these constituents remains a disjointed and machinery-intensive process, relying on…
Austin Hartman, Rahul Satija
The burgeoning interest in in situ multiplexed gene expression profiling technologies has opened new avenues for understanding cellular behavior and interactions. In this study, we present a comparative benchmark analysis of six in situ gene expression profiling methods, including both commercially available and…
Abdulraouf Abdulraouf, Weirong Jiang, Zihan Xu, Zehao Zhang + 4 more
Spatial transcriptomics has revolutionized our understanding of cellular network dynamics in aging and disease by enabling the mapping of molecular and cellular organization across various anatomical locations. Despite these advances, current methods face significant challenges in throughput and cost, limiting their…
Yingying Lu, Qin Chen, Lingling An
The advent of spatial transcriptomics technology has allowed for the acquisition of gene expression profiles with multi-cellular resolution in a spatially resolved manner, presenting a new milestone in the field of genomics. However, the aggregate gene expression from heterogeneous cell types obtained by these…
Lambda Moses, Lior Pachter
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and tumors depends on the spatial organization of their cells. In the past decade high-throughput technologies have been developed to quantify gene expression in space, and computational methods have been developed that leverage…