spatial transcription data of papillary craniopharyngioma
After surgery brains tissiue was embedded in OCT and frozen in methylbutane cooled down using liquid nitrogen. Processing of slices and library preparation were performed for Visium as recommended by the manufacturer (10x Genomics). Two 10-m slices of anterior ATN and two 10-m slices of posterior ATN were placed on 10x Genomics Visium slides, fixed with methanol and labeled using NeuN 488 conjugated antibody (1:100, Abcam, RRID: AB_2716282) and DAPI (0.2 mg/mL, Sigma). Images were acquired using a 10 objective on a Zeiss LSM 880 confocal microscope. Images included fiducial frame in TRITC for spot alignment in downstream analysis. Slices were permeabilized for 24 min (previously optimized using samples of same genotype and age) and libraries were prepared according to the manufacturers user guide. Libraries were sequenced using an Illumina NextSeq2000 at a reading depth of 100M reads per sample using the following read metrics: Read1: 28bp; Index1: 10bp; Index2: 10bp; Read 2: 90bp