Slide-SeqV2 of patient sample: Sample MBM08_slide
RNA from 10 uM frozen tumor sections was extracted and spatially indexed as described in Stickels et al. (Nature Biotechnology, 2021). Briefly, sections were cut and then mounted on a "puck". RNA was hybridized for 15 min in 6x SCC and then reveres transcribed using Maxima RT.  Tissue was then digested and cleared using clearing buffer and proteinase K and unbound capture oligos were removed using EXO-I treatment. 2nd strand synthesis was then performed using sn-SMRT oligos and Klenow Enzyme and the libraries were amplified using PCR with Truseq and SMART PCR primers. Libraries after PCR amplification were tagmented and indexed using Nextera XT kit and Nextera N70x oligos. After SPRI cleanup libraries were quantified using D5000 tapestation and perpared for sequencing