In situ sequencing for RNA analysis in preserved tissue and cells

Ke, Rongqin, Mignardi, Marco, Pacureanu, Alexandra, Svedlund, Jessica, Botling, Johan, Wählby, Carolina, Nilsson, Mats·2013·Nature Methods
DOI 10.1038/nmeth.2563

Cited by (951)

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  19. Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications
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  22. In situ RNA-seq
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