Additional file 4: of RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

CNS cell type-specific genes from Zhang et al.’s study compared to the Sharma et al. study. Significant DE genes (DEG) identified as cell type-specific from the Zhang et al. study [69] were compared to CNS cell type-enriched proteins identified from the Sharma et al. study [60]. Each tab contains information on one specific CNS cell type. Within each tab, information is broken up by 3 parts: part 1 (highlighted in blue)—gene expression information on genes identified in this study, including WT and Mecp2 Jae/y FPKM values, Log2 fold change expression, and q-value (FDR); part 2 (highlighted in light orange)—gene identified as CNS cell type-specific in the Zhang et al. study [69] along with the respective gene’s fold change enrichment in the identified cell type relative to all other CNS cell types; and part 3 (highlighted in purple)—gene/protein identified as CNS cell type-specific in the Sharma et al. study [60] along with the respective gene’s fold change enrichment (Log2 fold expression and Log2 LFQ intensity) in the identified cell type relative to all other CNS cell types, −Log10 p-value, standard deviation in LFQ intensity, and UniProt accession identity (major protein IDs). For oligodendrocytic-enriched genes, genes enriched in oligodendrocyte precursor cells (OPC), newly formed oligodendrocytes, and myelinating oligodendrocytes from the Zhang et al. study [69] were combined under the broad category “oligodendrocyte-enriched.” For endothelial-enriched genes, only genes identified as endothelial-enriched genes from the Zhang et al. study [69] are provided since the Sharma et al. study [60] did not examine endothelial cells. File format: Microsoft Excel spreadsheet. (XLS 71 kb)