AI Article Synopsis
- Researchers developed a new technique called PBHL-seq that uses photo-irradiation to analyze gene expression in specific areas of tissue samples, allowing for detailed study of tissue complexity.
- This method involves hybridizing and sequencing cDNA using light-controlled oligonucleotides, producing spatially indexed transcriptomes from the targeted regions.
- PBHL-seq has successfully identified thousands of differentially expressed genes in mouse tissue samples, including subcellular areas, while keeping the samples intact for further research.
Article 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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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335973 | PMC |
| http://dx.doi.org/10.1038/s42003-024-06694-5 | DOI Listing |
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