Spatial transcriptomic analysis of Nf1+/- mouse brain

Regional differential gene expression analyses of brains from four 24w-old Nf1+/- mice 10 µm sections from fresh frozen, OCT embedded mouse brain tissue samples were collected on Visium Gene Expression Slides (10x Genomics, Pleasanton, CA). Sections were H&E stained and imaged (Keyence BZX 800). Sections were permeabilized for 10 minutes, followed by reverse transcription, cDNA synthesis, cDNA amplification and NGS library preparation as per manufacturer's protocol (10x Genomics, Pleasanton, CA). For sequencing, indexed libraries were pooled and sequenced over NovaSeq 6000 (Illumina inc. San Diego, CA) to obtain a minimum of 50,000 reads/spot (250 M reads/section). Raw sequencing reads were parsed through the Spaceranger analysis pipeline (10x Genomics, Pleasanton, CA) to generate the final readout.