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Spatial Transcriptomics Inc sequencing
Sequencing, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/spatial+transcriptomics+based+analysis/based+sequencing/pmc12317664-373-11-19
Average 86 stars, based on 1 article reviews
sequencing - by Bioz Stars, 2026-09
86/100 stars

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Article Title: CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data
Article Snippet: It is conceivable that this pipeline would also be compatible with sequencing-based spatial modalities (for example, Slide-seq, Stereo-seq, high-definition spatial transcriptomics 60 - 62 ), as such datasets are usually accompanied by H&E or fluorescent images of the same or an adjacent tissue section, on top of the spatially resolved genomic readouts; hence, inputs to the CellLENS pipeline can be further curated and tested in the future.

Article Title: Harnessing spatial transcriptomics to understand host-parasite interactions in plants and animals.
Article Snippet: In contrast, sequencing-based spatial transcriptomics technologies capture mRNA directly from tissue sections using spatial barcodes, followed by cDNA synthesis and high-throughput next-generation sequencing (You et al., 2024).

Article Title: SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process
Article Snippet: However, there is a notable phenomenon associated with the sequencing-based spatial transcriptomics technology called spot-swapping , where RNA molecules diffuse from their original locations to adjacent spots on a tissue slide ( (A)).

Generated:

Article Title: A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging-based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein-coding transcriptome [ , ] .

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single‐cell RNA sequencing (scRNA‐seq) and sequencing‐based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging‐based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein‐coding transcriptome [ , ].

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ 4 ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imagingbased spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the proteincoding transcriptome [ 5, 6 ].

Single Cell:

Article Title: A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging-based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein-coding transcriptome [ , ] .

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single‐cell RNA sequencing (scRNA‐seq) and sequencing‐based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging‐based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein‐coding transcriptome [ , ].

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ 4 ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imagingbased spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the proteincoding transcriptome [ 5, 6 ].

RNA Sequencing:

Article Title: A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging-based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein-coding transcriptome [ , ] .

Article Title: Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomics
Article Snippet: .. Notably, sequencing-based spatial transcriptomics technologies, a natural progression of single-cell RNA sequencing, have become popular methods of understanding transcriptome expression in a spatial context. ..

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single‐cell RNA sequencing (scRNA‐seq) and sequencing‐based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging‐based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein‐coding transcriptome [ , ].

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ 4 ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imagingbased spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the proteincoding transcriptome [ 5, 6 ].

Sequencing:

Article Title: A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging-based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein-coding transcriptome [ , ] .

Article Title: Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomics
Article Snippet: .. Notably, sequencing-based spatial transcriptomics technologies, a natural progression of single-cell RNA sequencing, have become popular methods of understanding transcriptome expression in a spatial context. ..

Article Title: SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments
Article Snippet: .. It is indeed noteworthy that the spatial transcriptomics technologies used in this study (Stereo-seq, Visium, and Slide-seq) are all 3’ end-based sequencing methods, which may introduce a bias toward detecting SNVs at the 3’ end and limit the ability to capture mutations across the entire gene. ..

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single‐cell RNA sequencing (scRNA‐seq) and sequencing‐based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging‐based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein‐coding transcriptome [ , ].

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ 4 ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imagingbased spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the proteincoding transcriptome [ 5, 6 ].

Spatial Transcriptomics:

Article Title: A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging-based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein-coding transcriptome [ , ] .

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ ] using various modalities, including single‐cell RNA sequencing (scRNA‐seq) and sequencing‐based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imaging‐based spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the protein‐coding transcriptome [ , ].

Article Title: A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.
Article Snippet: .. More recently, we generated an atlas of cells in the human tonsil [ 4 ] using various modalities, including single-cell RNA sequencing (scRNA-seq) and sequencing-based spatial transcriptomics, which was limited by its lateral resolution and unable to distinguish single cells in this regard. .. Nowadays, imagingbased spatial transcriptomics technologies can profile tissues at molecular resolution while retaining physical coordinates of both targets and cells; as of recent, they are able to resolve the proteincoding transcriptome [ 5, 6 ].

Expressing:

Article Title: Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomics
Article Snippet: .. Notably, sequencing-based spatial transcriptomics technologies, a natural progression of single-cell RNA sequencing, have become popular methods of understanding transcriptome expression in a spatial context. ..

Introduce:

Article Title: SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments
Article Snippet: .. It is indeed noteworthy that the spatial transcriptomics technologies used in this study (Stereo-seq, Visium, and Slide-seq) are all 3’ end-based sequencing methods, which may introduce a bias toward detecting SNVs at the 3’ end and limit the ability to capture mutations across the entire gene. ..



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Xenium-Based Spatial <t>Transcriptomics</t> Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm
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Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm

Journal: Biomarker Research

Article Title: Single-cell, single-nucleus and xenium-based spatial transcriptomics analyses reveal inflammatory activation and altered cell interactions in the hippocampus in mice with temporal lobe epilepsy

doi: 10.1186/s40364-024-00636-3

Figure Lengend Snippet: Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections. A Whole-brain transcriptomic information obtained through Xenium-based spatial transcriptomics analysis, with reconstructed cell bodies displayed in different colours. The white box highlights the TLE and control hippocampal regions. B Enlarged view of the hippocampal region highlighted in A. C UMAP plot showing the 27 identified cell types. D - I High-resolution expression patterns of marker genes for astrocytes, microglia, oligodendrocytes, CA1 pyramidal neurons, dentate gyrus granule cells, and CA3 pyramidal neurons in Control and TLE sections. The left side represents the brain of a control mouse, while the right side represents the brain of a TLE mouse. Each red dot represents a positive expression point for a gene, with a diameter of 5 μm

Article Snippet: Fig. 6 Xenium-Based Spatial Transcriptomics Analysis of TLE and Control Mouse Brain Sections.

Techniques: Control, Expressing, Marker