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Search · four archives
7 papers · ranked by Valyu relevance
Vladyslav Honcharuk, Keiko Takemoto, Diego Diez, Shinpei Kawaoka + 1 more
The 10x Genomics Xenium platform enables high-resolution spatial transcriptomics at single-cell and subcellular scales, but effective reuse of public Xenium datasets is hindered by large data sizes and heterogeneous file formats. We previously developed DeepSpaceDB, a spatial transcriptomics database designed for…
Claudia Arnedo-Pac, Jo Heffer, Marina Golotiuk, Ania M. Piskorz + 1 more
Spatially resolved transcriptomics was named Method of the Year 2020^1^ and has continued to evolve rapidly since then, providing novel insights in development, physiology, and disease processes. Many approaches now offer excellent performance in formalin-fixed paraffin embedded tissue, opening up a wealth of archived…
Lixia Chen Wu, Xinyu Hu, Fengwei Zhan, Chuhanwen Sun + 6 more
Sequencing-based spatial transcriptomics technologies, including Visium HD and Stereo-seq, now enable transcriptome-wide profiling at subcellular resolution. However, these platforms generate measurements over spatially barcoded units rather than biologically segmented cells, creating a fundamental bottleneck for…
Yang Xu, Callum J. Sargeant, Yue You, Yupei You + 5 more
Spatial transcriptomics technology has developed rapidly in recent years, with various sequencing-based platforms such as 10x Visium, Slide-seq and Stereo-seq becoming widely used by researchers. Each platform brings its own set of protocols and customised data analysis pipelines which presents challenges when the goal…
Angelo Anacleto, Weiqiu Cheng, Qianlu Feng, Chun-Seok Cho + 15 more
Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200–300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to…
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…
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Desorption Electrospray Ionization Mass Spectrometry Imaging (DESI-MSI) is a powerful technique for molecular analysis of surfaces; however, its application of single cell studies has not been previously published. In the current work, a commercial DESI setup (DESI XS) coupled to a mass spectrometer was used to analyze…