title: GSM8026853: Brain, Flu, rep1; Mus musculus; OTHER
library_construction_protocol: At 5 weeks and 5.5 weeks post-cuprizone, corresponding to peak demyelination and partial remyelination, respectively, brains were harvested, bisected sagitally, trimmed rostral to the fornix and caudal to the splenium of the CC, immediately frozen in a bed of finely crushed dry ice, and then embedded in Tissue-Tek® O.C.T. Compound (Sakura #4583) in a dry ice-ethanol slurry. Sagittal sections were cut on a cryostat microtome (Leica CM 1950) at 10 µm thickness and within 0-0.5 mm from the midline. Fresh, frozen sections were placed on slides (one replicate of each treatment per slide) containing spatially-barcoded oligonucleotide probes in a 6.5 x 6.5 mm area cDNA libraries were constructed according to manufacturer's instructions (Visium Spatial Gene Expression kit V1, 10x Genomics). Briefly, tissues were fixed, stained, and permeabilized on the slide and cDNA libraries were synthesized from captured RNA. They were pooled and sequenced on two S4 2x150nt lane in a NovaSeq 6000.  Read1 is 28nt in length, Read2 is 150nt in length and  indexes are 10nt in length