Journal: Cell Reports Medicine

Article Title: MicroRNA-dependent suppression of biological pacemaker activity induced by TBX18

doi: 10.1016/j.xcrm.2022.100871

Figure Lengend Snippet:

Article Snippet: Rabbit Polyclonal anti-HCN2 , Alomone Labs , Cat# APC-030 RRID: AB_2313726.

Techniques: Recombinant, Staining, Luciferase, Reporter Assay, Western Blot, Isolation, Plasmid Preparation, Software

Journal: Acta Neuropathologica Communications

Article Title: Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function

doi: 10.1186/s40478-023-01568-z

Figure Lengend Snippet: Statistical analysis methods and results for validation data

Article Snippet: We used following antibodies at indicated dilutions SPARC (Abcam, ab225716, RRID:AB_2924283, 1:100), OLIG2 (R&D Systems, AF2418, RRID:AB_2157554, 1:100), RBFOX1 (Abcam, ab243727, RRID:AB_2924285, 1:100), FMN1 (Abcam, ab244482, RRID:AB_2924284, 1:100), OPALIN (Abcam, ab121425, RRID:AB_11127935, 1:100), HCN2 (Alomone Labs, APC-030, RRID:AB_2313726, 1:1000), GPNMB (Abcam, ab227695, RRID:AB_2924286, 1:100), IBA1(ab178846, RRID:AB_2636859, 1:50).

Techniques:

Journal: Acta Neuropathologica Communications

Article Title: Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function

doi: 10.1186/s40478-023-01568-z

Figure Lengend Snippet: Oligodendroglia cluster segregation and validation. a Feature plots of subsetted oligodendroglia that qualitatively show the expression of lineage marker and cluster marker genes (scale bars show LogNormalized counts). PLP1 marks oligodendrocytes (Oligo) and PDGFRA oligodendrocyte precursor cells (OPCs). b Dot plot of a selection of marker genes for committed oligodendrocyte precursor cells (COP_A-C), oligodendrocyte precursors (OPC_A & B) and oligodendrocytes (Oligo_A-F) showing cluster segregation. The dendrogram visualizes the relationship of clusters based on 2000 most variable genes. c Validation of oligodendrocyte cluster markers by immuno-fluorescence stainings at the protein level. OLIG2-positive oligodendrocytes show either one cluster marker (fat arrow) or a second cluster marker (arrowhead), only with the occasional double-positive cell (thin arrow). SPARC-positive Oligo_F cells also express HCN2. d BaseScope duplex stainings for OPC cluster validation. Dotted line delineates the cell boundary with arrow pointing at cluster marker signal. PDGFRA marks all OPCs with PAX3 labelling OPC_A and NELL1, OPC_B. e, f Proportion of oligodendroglia expressing cluster markers by pairs in our snRNAseq dataset e colour-coded by single markers or overlap and f in the validation datasets by immunofluorescence (oligodendrocytes (OL), OLIG2 +) or BaseScope Duplex (OPCs – PDGFRA +), showing good concordance. For example, OL_F (cluster Oligo_F) is SPARC- positive but RBFOX1-negative (second bar in f ) and as positive for HCN2 and SPARC (5th bar in (f)). IF immuno-fluorescence, ISH In situ hybridization. g Violin plot showing that most HCN2 expression is in the Oligo_F cluster

Article Snippet: We used following antibodies at indicated dilutions SPARC (Abcam, ab225716, RRID:AB_2924283, 1:100), OLIG2 (R&D Systems, AF2418, RRID:AB_2157554, 1:100), RBFOX1 (Abcam, ab243727, RRID:AB_2924285, 1:100), FMN1 (Abcam, ab244482, RRID:AB_2924284, 1:100), OPALIN (Abcam, ab121425, RRID:AB_11127935, 1:100), HCN2 (Alomone Labs, APC-030, RRID:AB_2313726, 1:1000), GPNMB (Abcam, ab227695, RRID:AB_2924286, 1:100), IBA1(ab178846, RRID:AB_2636859, 1:50).

Techniques: Expressing, Marker, Selection, Fluorescence, Immunofluorescence, In Situ Hybridization

Journal: Acta Neuropathologica Communications

Article Title: Brain matters: unveiling the distinct contributions of region, age, and sex to glia diversity and CNS function

doi: 10.1186/s40478-023-01568-z

Figure Lengend Snippet: Regional variation in the oligodendroglial population. Differential abundance analysis using Milo shows regional differences between a CSC and BA4, b CB and BA4 and c CB and CSC. Significant increases are coloured in red/blue according to region (FDR < 0.1). Each dot represents a neighbourhood consisting of an average of 50–100 cells. OPC_A is more abundant in CB and CSC, and OPC_B in BA4. Oligo_C and Oligo_F are enriched in the spinal cord compared to the other regions. Oligo_F is a smaller cluster but strikingly different from the other oligodendrocytes in its transcriptome including genes associated with astrocytes (such as SPARC) and Schwann cells (MPZ) while clearly not being an astrocyte or Schwann cell based on the absence of relevant lineage markers. d, e Quantification by immunofluorescence (shown in Fig. c) showing the increased abundance of Oligo_F in the human spinal cord using the markers d SPARC + OLIG2 + RBFOX1- and e HCN2 + SPARC + OLIG2 + . f, g Quantification by BaseScope duplex of regional selectivity of OPC_A and B (example in Fig. d) showing that f PAX3 -positive OPC_A are more abundant in CB and CSC and g NELL1 -positive OPC_B are BA4 specific. Plots visualize percentage of total OLIG2 d , e or PDGFRA f , g -positive cells. Boxes in plots visualize median and 25th and 75th percentiles and whiskers mark range up to 1.5 * inter-quartile ranges to show potential outliers. See Table for number of samples, statistical tests used and results and Addtional file : Table S2 for sample information. h Volcano plot showing differential gene expression between BA4 OPC_B and CSC OPC_A. i Gene ontology analysis based on differentially expressed genes of CSC OPC_A in comparison to BA4 OPC_B as shown in h) (complete version in Additional file : Fig. S7). Differentially expressed genes in oligodendrocytes (oligos) with tissue region j–l with red arrows indicating genes that are discussed in the main text. m Gene ontology terms of genes enriched in spinal cord oligodendrocytes in comparison to brain oligodendrocytes. (Complete version in Additional file : Fig. S8)

Article Snippet: We used following antibodies at indicated dilutions SPARC (Abcam, ab225716, RRID:AB_2924283, 1:100), OLIG2 (R&D Systems, AF2418, RRID:AB_2157554, 1:100), RBFOX1 (Abcam, ab243727, RRID:AB_2924285, 1:100), FMN1 (Abcam, ab244482, RRID:AB_2924284, 1:100), OPALIN (Abcam, ab121425, RRID:AB_11127935, 1:100), HCN2 (Alomone Labs, APC-030, RRID:AB_2313726, 1:1000), GPNMB (Abcam, ab227695, RRID:AB_2924286, 1:100), IBA1(ab178846, RRID:AB_2636859, 1:50).

Techniques: Immunofluorescence, Expressing