title: GSM7511116: Pancreas, CIP injected, 30 days, rep5; Mus musculus; OTHER
library_construction_protocol: For GeoMx WTA profiling, we generated two 12-core tissue blocks containing each time point. Formalin-fixed paraffin-embedded tissue sections (5 μm) were processed according to the Nanostring Manual Slide Preparation guide (MAN-10150-01). A total of 57 regions of interest (ROIs, 650 μm x 650 μm) were profiled, with 2-4 ROIs selected from each tissue sample. The GeoMX Digital Spatial Profiler instrument selectively illuminated each ROI with UV light, permitting the photocleavage of a 66 bp-long DNA barcode from each oligonucleotide probe that was hybridized to an mRNA target within the ROI. The DNA barcodes from each ROI were deposited in a collection plate, and PCR was used to uniquely index each ROI's barcodes with specific Illumina i5/i7 dual indexing primers. Amplified, indexed libraries were then pooled, purified with SPRI beads (Beckman Coulter) and the library quality assessed by capillary electrophoresis using a Fragment Analyzer (Agilent). Paired-end sequencing was performed on a NovaSeq6000 (Illumina), targeting the Nanostring recommended read depth of 2.5 billion read-pairs (calculated using the sum of each ROI's area).