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Additional file 1. Appendix

Additional file 3: Table S3. GR methylation in U and C regions for patients by outcome.

Additional file 2. Supplemental Table 2: DEPICT genetic association in pathways.

Control data of optogenetic activation of ACC PV-positive interneurons. A, Result of the PV-ChR2 saline group. There was no light effect either before (off: 5.09 ± 0.22 g, on: 4.84 ± 0.09 g; n = 6) or after saline injection (off: 5.18 ± 0.18 g, on: 4.79 ± 0.23 g; n = 6). B, Result of the WT-ChR2 CFA group. There was no light effect before (off: 5.18 ± 0.13 g, on: 5.12 ± 0.12 g; n = 8) or after CFA (off: 3.33 ± 0.12 g, on: 3.58 ± 0.19 g; n = 8). There was only statistically significant effect of CFA treatment per se (p 

Additional file 12: Table S1. Total number of ones, zeros and nulls in the sparse matrix for the 163 TFs used in this study.

Additional optimization code (MATLAB). (TXT 2Â kb)

Additional file 8: Supplementary Movie 1. Description: Time-lapse imaging of GFP-0N4R reporter cells seeded with S1 brain fractions including no seed-competent tau derived from aged non-transgenic mice. Images were obtained for 12 hours 30 min (10 min/frame for 75 frames). Scale bars, 10 μm.

Additional file7: Table S18. DNAmeQTL analysis for the loci significantly associated with DNAme-based XCI status calls. See additional files. These loci were independently tested as DNAmeQTLs in females and males, with some columns color coded based on sex (pink female, light blue male). There are also columns with the median and mean DNAme value at the gene’s island for samples with the reference or alternate allele at that loci; these columns are color coded based on whether the allele is in the range to escape from XCI (DNAme<0.01, blue) or in the range to be subject to XCI (DNAme>0.15, orange). There are mean and median columns for both males and females, but only the female columns are color coded based on XCI status. There are boxes around the genes with female median values with one allele in the range to escape XCI and the other allele in the range to be subject to XCI.

AUC performance can be predicted for high p/n data using parameters as variables. Prediction accuracy using the random forest classifier for high p/n validation data with Gini importance measures. (a) The combined validation data demonstrated a strong correlation between the predicted and observed AUC values (ρ = 0.48, p 

Comparison of gene expression of CD4+ T cells separated from PBMC isolated using CPT and Ficoll. A two-group comparison with permutation analysis for differential expression was performed, as described in Methods, on microarray data to identify differentially expressed genes between CD4+ T cells separated from CPT- and Ficoll-isolated PBMC. Probsets are ranked according to the FDR value. (CSV 26355 kb)