Journal: Immunity

Article Title: Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system.

doi: 10.1016/j.immuni.2024.07.001

Figure Lengend Snippet: Figure 6. HDAC1/2 depletion in microglia improves remyelination in aged mice (A) Schematic representation of experimental paradigm in Cx3cr1creERT/hetHdac1fl/flHdac2fl/flaged mice. (B) Quantitative PCR analysis of Hdac1 and Hdac2 in CD11b+ cells isolated from Cre and Cre+ mice 2 weeks after tamoxifen induction. (C) Images of MAC2+IBA1+ cells in the demyelinated lesions at 4 dpi. Scale bars, 50 mm. (D) Quantification of the percentage of MAC2+IBA1+ cells over IBA1+ cells in the demyelinated lesion at 4 dpi. (E) Images of MHCII+IBA1+ cells in the demyelinated lesions at 4 dpi. Scale bars, 50 mm. (F) Quantification of the percentage of MHCII+IBA1+ cells over IBA1+ cells in the demyelinated lesion at 4 dpi. (G) Images of corpus callosum lesions in aged (12 months) Cre (control) and Cre+ (knockout) mice at 14 dpi. Scale bars, 200 mm. (H) Quantification of lesion volume and IBA1+ volume in aged (12 months) Cre (control) and Cre+ (knockout) mice at 14 dpi. (I) Quantification of CC1+OLIG2+ cells per mm2 of lesion at 14 dpi.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER High Sensitivity NGS Fragment Analysis Kit Agilent Cat# DNF-474 DNA Clear & Concentrator TM-5 kit Zymo-research Cat# D4014 IP-Star Compact Automated System Diagenode Cat# B03000002 MicroPlex Library Preparation Kit v3 /96 rxns Diagenode Cat# C05010002 Qubit dsDNA HS Assay Kit Thermofisher Scientific Cat# Q32854 HDAC1 Fluorogenic Assay Kit BPS bioscience Cat#50061 HDAC2 Fluorogenic Assay Kit BPS bioscience Cat#50062 Deposited data Raw and analyzed data This paper GEO (GSE230187, GSE230190, GSE230191, GSE230480, GSE247529) Experimental models: Organisms/strains Mouse: C57BL/6JRj JANVIER labs RRID:IMSR_RJ:C57BL-6JRJ Mouse: Cx3cr1creERT2x Hdac1,2flox Datta et al.47 N/A Oligonucleotides Primers Table S4 N/A Software and algorithms R https://www.r-project.org/ RRID:SCR_001905 R studio https://www.rstudio.com/ Version 4.2 and 4.3 LIGER Welch et al.64 RRID:SCR_018100 Cell ranger 10x genomics v(6.1.0); RRID:SCR_017344 Doublet finder McGinnis et al.65 v(2.0.2); RRID:SCR_018771 scCustomise https://doi.org/10.5281/zenodo.5706430 RRID:SCR_024675 Seurat Satija et al.66 v(4.0.6; 4.4.0); RRID:SCR_016341 Galaxy https://usegalaxy.eu/ RRID:SCR_006281 IGV Robinson et al.67 RRID:SCR_011793 Trim galore http://www.bioinformatics. babraham.ac.uk/ projects/trim_galore/ RRID:SCR_011847 Cutadapt Martin68 RRID:SCR_011841 Bowtie2 Langmead and Salzberg69 RRID:SCR_016368 BAM tools Barnett et al.70 RRID:SCR_015987 Picard tools http://broadinstitute.github.io/picard RRID:SCR_006525 Deep tools Ramı́rez et al.71 RRID:SCR_016366 MACS2 Zhang et al.72 RRID:SCR_013291 Csaw Lun and Smyth73 https://doi.org/10.1093/nar/gkv1191 FindMotifsGenome tool Heinz et al.74 http://homer.ucsd.edu/homer/motif/ STAR Dobin et al.75 RRID:SCR_004463 Feature counts Liao et al.76 RRID:SCR_012919 Deseq2 Love et al.77 RRID:SCR_015687 Gene ontology (GO) enrichment analysis http://www.geneontology.org RRID:SCR_002811 scCODA B€uttner et al.78 https://github.com/theislab/scCODA Revigo Supek et al.79 RRID:SCR_005825 Cytoscape https://cytoscape.org/ RRID:SCR_003032 Graph Pad Prism https://www.graphpad.com/ RRID:SCR_002798 Image Lab Software Bio-Rad RRID:SCR_014210 ImageJ (Fiji) Schindelin et al.80 RRID:SCR_002285 Adobe Illustrator https://www.adobe.com/ RRID:SCR_010279 Code for calculating the lesion volume Bosch-Queralt et al.81 https://github.com/lenkavaculciakova/ lesion_volume (Continued on next page) e2 Immunity 57, 1–18.e1–e8, September 10, 2024

Techniques: Real-time Polymerase Chain Reaction, Isolation, Control, Knock-Out