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| Main Authors: | , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Genome research
2025
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/40764053/ |
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| _version_ | 1868266169487589378 |
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| author | Dong, Xue Hu, Mengzhu Cui, Xiaonan Zhou, Wenjian Cai, Jingtao Mao, Guangyao Shi, Weiyang |
| author_facet | Dong, Xue Hu, Mengzhu Cui, Xiaonan Zhou, Wenjian Cai, Jingtao Mao, Guangyao Shi, Weiyang Dong, Xue Hu, Mengzhu Cui, Xiaonan Zhou, Wenjian Cai, Jingtao Mao, Guangyao Shi, Weiyang |
| collection | PubMed - marine biology |
| contents | High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow. Dong, Xue Hu, Mengzhu Cui, Xiaonan Zhou, Wenjian Cai, Jingtao Mao, Guangyao Shi, Weiyang Animals Mice Gene Expression Profiling Transcriptome Workflow Tissue Fixation Paraffin Embedding Cost-Benefit Analysis Embryo, Mammalian The spatial heterogeneity of gene expression has driven the development of diverse spatial transcriptomics technologies. Here, we present photocleavage and ligation sequencing (PCL-seq), a spatial indexing method utilizing a light-controlled DNA labeling strategy applied to tissue sections. PCL-seq employs photocleavable oligonucleotides and ligation adapters to construct transcriptional profiles of specific regions of interest (ROIs) designated via microscopically controlled photo-illumination. In frozen mouse embryos, PCL-seq generates spatially aligned gene expression matrices and produces high-quality data, detecting approximately 170,000 unique molecular identifiers (UMIs) and 8600 genes (illumination diameter = 100 µm). Moreover, PCL-seq is compatible with formalin-fixed paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae of mouse embryo FFPE sections. Additionally, PCL-seq achieves subcellular resolution, as demonstrated by differential expression profiling between nuclear and cytoplasmic compartments. These characteristics establish PCL-seq as an accessible and versatile workflow for spatial transcriptomic analyses in both frozen and FFPE tissues with subcellular resolution. |
| format | Artículo científico |
| id | pubmed_40764053 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Genome research |
| record_format | pubmed |
| spellingShingle | High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow. Dong, Xue Hu, Mengzhu Cui, Xiaonan Zhou, Wenjian Cai, Jingtao Mao, Guangyao Shi, Weiyang Animals Mice Gene Expression Profiling Transcriptome Workflow Tissue Fixation Paraffin Embedding Cost-Benefit Analysis Embryo, Mammalian High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow. Dong, Xue Hu, Mengzhu Cui, Xiaonan Zhou, Wenjian Cai, Jingtao Mao, Guangyao Shi, Weiyang Animals Mice Gene Expression Profiling Transcriptome Workflow Tissue Fixation Paraffin Embedding Cost-Benefit Analysis Embryo, Mammalian The spatial heterogeneity of gene expression has driven the development of diverse spatial transcriptomics technologies. Here, we present photocleavage and ligation sequencing (PCL-seq), a spatial indexing method utilizing a light-controlled DNA labeling strategy applied to tissue sections. PCL-seq employs photocleavable oligonucleotides and ligation adapters to construct transcriptional profiles of specific regions of interest (ROIs) designated via microscopically controlled photo-illumination. In frozen mouse embryos, PCL-seq generates spatially aligned gene expression matrices and produces high-quality data, detecting approximately 170,000 unique molecular identifiers (UMIs) and 8600 genes (illumination diameter = 100 µm). Moreover, PCL-seq is compatible with formalin-fixed paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae of mouse embryo FFPE sections. Additionally, PCL-seq achieves subcellular resolution, as demonstrated by differential expression profiling between nuclear and cytoplasmic compartments. These characteristics establish PCL-seq as an accessible and versatile workflow for spatial transcriptomic analyses in both frozen and FFPE tissues with subcellular resolution. |
| title | High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow. |
| topic | Animals Mice Gene Expression Profiling Transcriptome Workflow Tissue Fixation Paraffin Embedding Cost-Benefit Analysis Embryo, Mammalian |
| url | https://pubmed.ncbi.nlm.nih.gov/40764053/ |