GSM6716965: 19G0635, Patient 3, Spatial Transcriptomics (Visium); Homo sapiens; RNA-Seq
Selected formalin-fixed paraffin-embedded (FFPE) tumor samples were firstly analyzed for RNA quality by evaluating the percentage of fragments with a length greater than 200 nucleotides (DV200). Samples with a DV200 higher than 50% were considered as usable for Visium analysis Briefly, one to two 10 µm-thin FFPE sections were cut, dewaxed and lysed. RNA was extracted and purified using the High Pure FFPE RNA Isolation Kit (cat. no.: 06650775001, Roche) and analyzed by microfluidics-based automated electrophoresis (Bioanalyzer; Agilent) All samples tested in this study had a DV200 > 50%. Serial sections, stained with Hematoxylin Eosin Saffron (HES), were used to identify an area of ~6 x 6 mm containing liver metastasis, in order to provide optimal coverage of the 6.5 x 6.5 mm capture area on the Visium slide. Following macrodissection, 10 µm-thin sections of the selected areas were fixed on the Visium slide, dewaxed, HES-stained, imaged, and decrosslinked according to manufacturer's instruction (10X Genomics Visium Spatial Gene Expression for FFPE kit, Human Transcriptome, Protocol no.: GC000408 and GC000409). Library preparation was then carried out according to manufacturer's instruction (Protocol no., GC000407)