ScRNAseq of Mertk-WT and Mertk-KO corpus callosum

ABSTRACT: Purpose: The goal of this study is to characterize the the different CNS cell types in the mouse corpus callosum over three different cuprizone treatment timepoints - (Baseline, 4 weeks, 4 weeks + 3 weeks of recovery) and compare the Mertk-WT vs Mertk-KO response to demyelination. Methods: 3-4 biological replicates (mice) were used for each timepoint/genotype. Tissues were dissociated into single cells for preparation of 10X libraries and sequenced with HiSeq 2500 (Illumina). Results: scRNA-Seq data were analyzed with an in-house analysis pipeline. Briefly, reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique molecular identifiers (UMIs) for reads overlapping exons in sense orientation. To account for sequencing or PCR errors, one mismatch was allowed when collapsing UMI sequences. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Cells with less than 1000 total UMIs were discarded. Conclusions: We show differences between Mertk-WT and Mertk-KO cellular profiles, particularly at the 4 week Cuprizone timepoint. In addition, our data show a distinct, yet heterogenous, population of oligodendrocytes that arise in the cuprizone model where remyelination is spontaneous and robust. Our results provide new insights into the cellular response to demyelination, that includes a resource for comparing and interpreting neurodegenerative disease models.

ORGANISM(S): Mus musculus

PROVIDER: GSE148676 | GEO | 2021/04/13

REPOSITORIES: GEO