Fig. 1. Workflow for RNA and exome sequencing on MALDI-MSI-processed FFPE tissue sections.

For examinations of the effect of the MSI workflow on the genome and transcriptome, the FFPE samples were sectioned and subsequently processed in three different approaches. As a control approach, one sample was extracted directly after dissection (FFPE) and one sample was dissected and stained with hematoxylin and eosin (FFPE-HE). In the discovery approach, MSI with an additional HE staining was performed to follow the regular procedure of an MSI experiment (FFPE-MSI). After scanning the stained tissue for the MSI procedure, the same tissue was used for the extraction of gDNA and total RNA. Then the integrity of the nucleic acids was examined, the libraries were prepared and the samples were sequenced accordingly.