GSM5585203: Slide1_4_B1; Mus musculus; OTHER
Mouse spinal cords were embedded in OCT and cryosections were generated at 10 µm at −20 °C. Sections were immediately placed on chilled Visium Tissue Optimization Slides (catalog no. 1000193, 10x Genomics) or Visium Spatial Gene Expression Slides (catalog no. 1000184, 10x Genomics). Tissue sections were then fixed in chilled methanol and stained according to the Visium Spatial Gene Expression User Guide (catalog no. CG000239 Rev A, 10x Genomics) or Visium Spatial Tissue Optimization User Guide (catalog no. CG000238 Rev A, 10x Genomics). For gene expression samples, tissue was permeabilized for 12 min , which was selected as the optimal time based on tissue optimization time-course experiments. Brightfield histology images were taken using a 10× objective on a slide scanner (Olympus VS-120 Slide scanner). For tissue optimization experiments, fluorescent images were taken with a TRITC filter using a 10× objective and 400-ms exposure time. Spatial transcriptomics libraries were prepared according to the Visium Spatial Gene Expression User Guide. They were then clustered at 270 pM on a paired-end HiSeq4000 flow cell and sequenced on a HiSeq4000 System (Illumina) at a sequencing depth of approximately 140–180 Mio read per sample. Sequencing was performed using the following read protocol: read 1: 28 cycles; i7 index read: 8 cycles; i5 index read: 8 cycles; and read 2: 98 cycles.