title: colon_full_roi7
organism: Homo sapiens
description: Protocols: Slides for Nanostring analysis were prepared from formalin-fixed paraffin-embedded tissues. Multiple tissues were combined on a single slide to allow simultaneous analysis. Nanostring data was collected from two separate slides consisting of representative tissues collected from different in vivo transplantation timepoints (slide1) and a reference normal adult human colon. Each Nanostring slide consisted of two to six different pieces of tissue. Slides were stained with pan-cytokeratin (Nanostring) and DAPI stains and then hybridised with Cancer Transcriptome Atlas probes. The slides were kept hydrated at all times. The slides were then loaded onto the Nanostring GeoMX data spatial profiler (DSP). Areas of illumination (AOI) were selected based on areas of relevant morphology, such as apical and basal crypt regions. Automated segmentation was also performed based on cytokeratin expression. Each AOI was selected to contain at least 100 predicted cells (nuclei) based on DAPI staining. Having selected the AOIs for each slide, automated harvesting was performed on the DSP and probes were collected in 96 well plates each with well-specific barcodes.  Library preparation was performed according to manufacturer's instructions for NanoString GeoMX DSP.