Data files

Around 15,000 CD45lowSiglec-H+ and CD45-O1+ single cells were sorted per sample using a FACSAria III (BD Biosciences) before being encapsulated into droplets with the Chromium Controller (10x Genomics) and processed according to the manufacturer’s specifications. Briefly, every transcript captured in all the cells encapsulated with a bead was uniquely barcoded using a combination of a 16-base pair (bp) 10x barcode and a 10-bp unique molecular identifier (UMI). Complementary DNA libraries ready ...

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 ...

Study of oligodendrocytes and microglia in aging in a tissue-specific manner (white and gray matter) using the 10X single-cell RNA-sequencing platform. We also analyzed Rag1-deficient mice to study how the lack of mature T cells affect the age-dependent glial alterations that occur in the white matter.

Study of microglia in aging and in a tissue specific manner (white and grey matter) using Smart-seq2 and 10x scRNA-seq technologies. We also analysed, 5xFAD mice (AD model) with Smart-seq2, and Apoe-KO with 10x transcriptomics. Additionally we studied the impact of Actinomycin-D during tissue dissociation on gene expression in microglia using Smart-seq2.

Grey and white matter (corpus callosum) were dissected from the brain of 4 months and 21 months old wild type mice, single cell suspension was isolated using Neural Tissue Dissection kit (myelin was removed on percoll gradient) then microglia cells were isolated using CD11b microbeads by Magnetic separation with MS columns (MACS technology).The cell pellets are resuspended in the RLT buffer (100ul-150ul), snap frozen in liquid nitrogen and stored in -80 freezer. RNA was extracted and transcriptome ...

RNA-seq of sorted cells from brain of Cortical MS mouse treated with vehicle or CSF1R inhibitor

To study the effect of the Grk2 or Ets1 KOs in rat and human CD4+ T cells, in vivo or in vitro respectively, we generated KO CD4+ T cell lines by CRISPR-RNP nucleofection (with an gRNA targeting the gene locus) or control (with a non-targeting gRNA) 3' bulk RNAseq was conducted on CD4+ T-MBP rat cells isolated form spleen or spinal cord parenchyma three days after co-transfer of control and KO cells into the animal. Cells were FACS sorted based on their fluorescent protein reporters, BFP for ...