Single-cell RNA-seq analysis of microglial cells in demyelinated corpus callosum

CX3CR1-GFP mice were fed with cuprizone for 4 weeks to induce brain demyelination. The central and lateral parts of the corpus callosum (CC) were then separately dissected, dissociated and GFP+ microglial cells were isolated by FACS. 2133 migroglial cells from medial CC and 2304 cells from lateral CC were then processed for single-cell RNA-seq analysis. Single Cell RNA sequencing library were generated using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500. FACS sortedmicroglial cells were processed using the Chromium Single Cell Controller (10X genomics, Pleasanton). Libraries were generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions. Analysis using molecular indexing information provides an absolute digital measurement of gene expression levels. Sequencing was performed using a NextSeq 500 Illumina device (2samples) containing transcript lengh of 57 bp.Droplet Based