Data files

Brain hemispheres were dissected from 6-month-old animals and subjected to single-nuclei RNA sequencing using 10x genomics Chromium 3’ assay. In total 4 genotypes were included for the experiment (WT, Cnp-/-, 5xFAD, Cnp-/-x5xFAD), each genotype has n=2 replicates.

Cortex and corpus callosum were dissected from every two animals (3-month-old) and pooled into one sample for single-nuclei RNA sequencing using 10x genomics Chromium 3’ assay. Each genotype has 2 replicates (in total n=4 animals).

Current spatial transcriptomics methods provide molecular and spatial information but no morphological readout. Here, we present STEM - a method that correlates multiplexed error-robust FISH with electron microscopy from neighboring tissue sections of the same sample. STEM links transcriptional and spatial organization of single cells with ultrastructural morphology of the tissue in vivo. Using STEM to characterize demyelinated white-matter lesions allowed us to link morphology of myelin-laden ...

Tryptic in solution digestion of the purified myelin fraction was performed according to the filter-aided sample preparation (FASP) protocol (Erwig et al., 2019) originally described by Manza et al., 2005; followed by LC-MS-analysis. In brief, purified myelin fractions corresponding to 10 µg myelin protein were dissolved and lysed in lysis buffer (1% ASB-14, 7 M urea, 2 M thiourea. 10 mM DTT 0.1 M Tris pH 8.5). Homogenised samples were diluted with lysis buffer containing 2% CHAPS to reduce ASB-14 ...

CUT&tag sequencing of mouse BM monocytes and HSPC-enriched myeloid cells from mice one month after stroke or control conditions was performed

Bulk mRNA sequencing of human heart paraffin embeded samples from stroke patients and control patients

Bulk ATAC sequencing of mouse HSPC-enriched BM cells treated with recombinant IL-1b or vehicle