GSM8694509: MC38_aPD1_R_m16_sec1_spatial; Mus musculus; OTHER
5 uM FFPE sections were cut on a microtome and placed on 10X Genomics Visium gene expression capture slides, and followed the Visium for FFPE manufacturer's protocol (10X Genomics CG000407|Rev D, non-cytassist) for the sample labeled "base_protocol". For the rest of the samples, there was an added permeabilization step during RNA Digestion. A blend of collagenase B and dispase enzymes (EMD Millipore Sigma #SCR140) resuspended in Hank's Buffered Salt Solution (ThermoFisher Scientific cat# 14175095) was added to the RNase buffer and enzyme mix to a concentration of 0.4 CDU/uL in step 3.1 to improve the permeabilization of the tissue. Then, after permeabilization at step 3.1.n, the slide was washed with 2X saline-sodium citrate buffer (Millipore Sigma S6639) with 0.1% sodium dodecyl sulfate (Millipore Sigma 71736). Libraries were constructed according to the Visium for FFPE mouse probeset manufacturer's protocol (non-cytassist)