Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Additional file 7: Fig. S5A. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). A Significant differentially methylated CpGs in BCL11B (T-LGLL compared to CD8+. memory T cells) were located in the gene body and assigned as enhancers by ENCODE, which match as enhancers in CD8-positive memory cells.

Additional file 8: Fig. S5B. (A and B): Location of differentially methylated CpG loci in the genes BCL11B and C14orf64 (LINC01550). B Significant differentially methylated CpGs in C14orf64 (LINC01550) (T-LGL compared to CD8 pos. memory T cells).

Supplementary Figure S2.Boxplot for P. lutea and I. palifera MAGs completeness and contamination stats..

Supplemental material, sj-tiff-2-tan-10.1177_17562864221143834 for Parkinson’s disease or multiple system atrophy: potential separation by quantitative susceptibility mapping by Franz Marxreiter, Vera Lambrecht, Angelika Mennecke, Jannis Hanspach, Jelena Jukic, Martin Regensburger, Juergen Herrler, Alexander German, Jan Kassubek, Georg Grön, Hans-Peter Müller, Frederik B. Laun, Arnd Dörfler, Juergen Winkler and Manuel A. Schmidt in Therapeutic Advances in Neurological Disorders

Supplementary Figure S2.Boxplot for P. lutea and I. palifera MAGs completeness and contamination stats..

Figure 2. Phylogenetic tree of bacterial MAGs with representation of different categories of Eukaryotic-like proteins (ELPs) from a) P. lutea and b) I. palifera. From inner to outer, Innermost circle represents MAGs color coded at bacterial class level, heatmap represents different ELP categories (Inner to outer: HEAT repeats; WD domain repeats, WD40; Ankyrin Repeats, ARPs; and Tetratricopeptide repeats, TPRs) and Bar plot represent total ELP counts in MAGs. Bars colored in “sky blue” represent MAGs...

Supplementary Figure S3.Stacked barplots for Relative abundance (>1%) of MAGs taxonomic classes for P. lutea and I. palifera. p_Aenigmatarchaeota, p_Nanoarchaeota, p_Thermoproteota represents the Archaea domain.

Figure 3. Phylogenetic tree of bacterial MAGs representing functional pathways based on nitrogen, sulphur and anoxygenic photosynthesis KEGG modules in a) P. lutea and b) I. palifera. From inner to outer ring, Innermost circle represents MAGs color coded at bacterial class level. Heatmap represents different KEGG modules (from inner to outer) for Nitrogen metabolism (M000175, M00524, M00529, M00530 and M00531), Sulfur metabolism (M00596, M00176 and M00595) and Anoxygenic photosynthesis (M00597). MAGs with at least one...

Figure 2. Phylogenetic tree of bacterial MAGs with representation of different categories of Eukaryotic-like proteins (ELPs) from a) P. lutea and b) I. palifera. From inner to outer, Innermost circle represents MAGs color coded at bacterial class level, heatmap represents different ELP categories (Inner to outer: HEAT repeats; WD domain repeats, WD40; Ankyrin Repeats, ARPs; and Tetratricopeptide repeats, TPRs) and Bar plot represent total ELP counts in MAGs. Bars colored in “sky blue” represent MAGs...

Figure 3. Phylogenetic tree of bacterial MAGs representing functional pathways based on nitrogen, sulphur and anoxygenic photosynthesis KEGG modules in a) P. lutea and b) I. palifera. From inner to outer ring, Innermost circle represents MAGs color coded at bacterial class level. Heatmap represents different KEGG modules (from inner to outer) for Nitrogen metabolism (M000175, M00524, M00529, M00530 and M00531), Sulfur metabolism (M00596, M00176 and M00595) and Anoxygenic photosynthesis (M00597). MAGs with at least one...

Additional file 3: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 5: Fig. S3B. Gene Ontology analysis of genes hyper- (A) and hypomethylated (B) of T-LGL patients. Significant Biological processes (GO database) enriched in genes associated with significantly differentially methylated CpG loci in T-LGL. Enrichment represented as odds ratio. Point size represents the gene count of each pathway. Enrichment p value obtained by overrepresentation analysis [30], represented by point color. B Gene Ontology analysis of hypomethylated genes in T-LGL.

Additional file 1: Figure S1. Glial CREB phosphorylation post injury is limited to IBA1+ cells. A)-B) AAVs are able to infect 89.98 ± 14.47% of cortical neurons. Data are shown as mean ± SD (Red dots represent individual animals). N=8. Scale bar: 50µm. C)-D) Non-neuronal pCREB signal is mainly found in IBA1+ cells (IBA1+ cells: 97.76 ± 0.83% vs. GFAP+ cells: 1.24 ± 0.83%). Data are shown as mean ± SD. N=4. Scale Bar: 50µm.E-F)...

Additional file 3: Figure S3. Blunting neuronal nuclear calcium signaling did not alter amplitude and velocity of whisker movement post-TBI. A)-C) The amplitudes of the affected (CS = 0.88 ± 0.22; CT = 1.1 ± 0.19; PS = 0.93 ± 0.42; PT = 1.269 ± 0.56) or unaffected (CS = 1.07 ± 0.39; CT = 1.05 ± 0.35; PS = 1.14 ± 0.45; PT = 1.22 ± 0.45) whisker were not significantly changed 24h after...

Additional file 4: Figure S4. Neuronal expression of osteoprotegerin is upregulated by nuclear calcium signaling and neuronal activity in TBI. A) Negative Control, baseline OPG (TNFRSF11B) signal and a positive Control of the in situ hybridization 24h post injury. B) OPG (TNFRSF11B) in situ signal is mainly found in neuronal sources (neuronal vs non-neuronal 75.38 ± 1.83% vs 24.62% ± 1.83%). N=5. C)-D) Significant increase of OPG (TNFRSF11b) mRNA density 24h post-TBI compared to sham...

Additional file 10: Fig. S6. Expression correlation between BCL11B & C14ORF64 (LINC01550). Expression correlation between BCL11B & C14ORF64 (LINC01550) in 426 human datasets with 42563 samples from R2: Genomics analysis and visualization platform (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi).