[Pubmed] Protocol to validate custom-designed BaseScope probes using cell-free synthesized protein lysates and in vitro-

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STAR Protoc. 2025 Oct 30;6(4):104180. doi: 10.1016/j.xpro.2025.104180. Online ahead of print.

ABSTRACT

BaseScope is an ultra-sensitive in situ hybridization technique specifically designed for detection of rare, short RNA molecules, particularly enabling co-detection of exon junctions in splice variants. Its use is cost intensive due to required protocol optimization for each tissue, especially when target expression is very low. Here, we present a protocol to validate functionality of custom-designed BaseScope probes by utilizing cell-free synthesized protein lysates and in vitro-transcribed purified mRNA as positive controls. We detail steps for slide preparation, probe hybridization, signal amplification, and detection.

PMID:41171757 | DOI:10.1016/j.xpro.2025.104180


Source: https://pubmed.ncbi.nlm.nih.gov/4117175 ... 22+67771e2