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

Journal: eLife

Article Title: Plasticity of gene expression in the nervous system by exposure to environmental odorants that inhibit HDACs

doi: 10.7554/eLife.86823

Figure Lengend Snippet: ( A ) Antennal and whole-mount brain staining of Gr63a-Gal4 flies. Flies were exposed to diacetyl (headspace from 10 –2 soln) or air for 2–5 d. Brains and antenna were dissected on the indicated days, fixed, and then stained for neuropil marker nc82 (red) and anti-GFP (green). Magnification 25 x. ( B ) Mean of ab1C neurons expressing GFP after indicated days of odor exposure. d4on = 2,3-butanedione. n = 6, error bars = SEM. Schematic chemical structures of diacetyl, β-hydroxybutyrate, and sodium butyrate. ( C ) Dose–activity curves of class I HDACs: HDAC1, HDAC2, HDAC3, HDAC8, and class II HDAC6 treated with various concentrations of diacetyl. Percentage of HDAC activity is relative to the activity of each enzyme without diacetyl. IC50s are indicated in the chart areas. Error bars = SEM, n = 4–5. ( D ) Representative structures of odorants that inhibit HDACs (left), and average percentage inhibition of class I HDACs: HDAC1, HDAC3, and class II HDAC4, HDAC6 treated with 15 mM of indicated volatiles (right). Error bar = SD, each tested in duplicate.

Article Snippet: Commercial assay or kit , HDAC2 Fluorogenic Assay Kit , BPS Bioscience , 50062 , .

Techniques: Staining, Marker, Expressing, Activity Assay, Inhibition

Journal: eLife

Article Title: Plasticity of gene expression in the nervous system by exposure to environmental odorants that inhibit HDACs

doi: 10.7554/eLife.86823

Figure Lengend Snippet:

Article Snippet: Commercial assay or kit , HDAC2 Fluorogenic Assay Kit , BPS Bioscience , 50062 , .

Techniques: Sequencing, Activity Assay, Isolation, SYBR Green Assay, Protease Inhibitor, Western Blot