ArticleCommunications biology2024
Large field of view and spatial region of interest transcriptomics in fixed tissue.
Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- SpatialFinder: a human-in-the-loop vision-language framework for prioritizing high-value regions in spatial transcriptomics.Frontiers in bioinformatics · 2026Article
- High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow.Genome research · 2025Article
- Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
5 authors.
Funding
Abstract
Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and formalin fixation and paraffin embedding (FFPE) tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis to promote the development of transcriptomics.
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Registered trials
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