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. Author manuscript; available in PMC: 2020 Nov 1.
Published in final edited form as: J Hepatol. 2020 Jun 10;73(5):1219–1230. doi: 10.1016/j.jhep.2020.06.004

Fig. 4. Model of in situ spatial transcriptomics.

Fig. 4

(A) Frozen liver tissue is cut and placed on a special slide special slide covered by beads carrying capture oligos composed by a polyd(T) tail for RNAs capture, a spatial barcode defining bead position, an UMI for transcript count, promoters and adaptors for cDNA synthesis, amplification and sequencing and a cleavage site to detach the oligos from the slide. B) The liver tissue on the spatial transcriptomics slide is fixed, stained by H&E and scanned by a conventional microscopy slide scanner. The tissue is lysed to release RNA, the capture oligos are cleaved and the libraries prepared as for scRNA-seq. The H&E image combined with data and coordinates of the spatial barcodes produce high-resolution single-cell gene expression data. GLUL encoding for glutamate-ammonia ligase is a known pericentral zonated gene and PCK1 encoding for phosphoenolpyruvate carboxykinase 1 is a periportal zonated gene. cDNA, complementary DNA; scRNA-seq, single-cell RNA-sequencing; UMI, unique molecule identifier.