Table 1. . Information of datasets we used in this study.
| Datasets (n samples) | Methyl450 datasets | Methyl27 datasets | EPIC datasets | |||||
|---|---|---|---|---|---|---|---|---|
| ROSMAP (743)† | GSE58885 (179)‡ | GSE74193 (673)§ | GSE38873 (153)¶ | BrainCloud (106)# | GSE26133 (160)†† | GSE93373 (16) | GSE86831 (15)‡‡ | |
| Number of batches | 2 | 16§§ | 5 | 14§§ | 4 | 10§§ | 2§§ | 4§§ |
| Number of positions | 12 | 12 | 12 | 12 | 12 | 12 | 8 | 8 |
| Tissue | FC | FC | DLPC (BA46/9) | CRBLM | CRBLM | LCLs | BCs, LCLs | T |
| Age, year | 88.01 ± 6.66 | -0.25 ± 0.07 | 36.13 ± 22.92 | 44.27 ± 9.84 | 35.86 ± 23.62 | NA | NA | NA |
| Number of females | 468 | 79 | 244 | 57 | 51 | 90 | 12 | NA |
| Race | 725 white, 14 AA, 1 N-A, 3 Asian | NA | 317 white, 356 AA | White | 42 white, 64 AA | Yoruba 160 | 16 Asian | NA |
| Affection status | 236 C, 507 AD | C | 224 C, 449 SZ | 47 C, 45 SZ, 15 Dep, 46 BP | C | C | 16 EBV | 2 C |
| Results | ||||||||
| ANOVA | Table 2 | Table 2 | Table 2 | Table 2 | Table 2 | Table 2 | Table 2 | Table 2 |
| Mean | Figure 2 | Supplementary Figure 5 | Supplementary Figure 3 | Supplementary Figure 5 | Supplementary Figure 5 | Supplementary Figure 4 | – | – |
| PVCA | Figure 3 | Supplementary Figure 6 | Supplementary Figure 6 | Supplementary Figure 8 | Supplementary Figure 8 | Supplementary Figure 8 | – | Supplementary Figure 7 |
| TRPs | – | – | Figure 4 | – | – | Figure 4 | – | – |
| DMPs | Figure 5 | – | – | – | – | – | – | – |
We used three methyl450, three methyl27 and two epic datasets from public databases and our own data to study the effects. Rosmap is the primary dataset we studied. The others are verified datasets. The ‘–’ means the datasets are not suitable for the special analyses.
‡Data taken from [11]
§Data taken from [41]
¶Data taken from [42]
#Data taken from [43]
††Data taken from [44]
‡‡Data taken from [45]
§§The batch is represented by batches information and sentrix_id, seperately.
AA: African–American; AD: Alzheimer’s disease; ANOVA: Analysis of variance analysis; BA: Brodmann area; BC: B cell; BP: Bipolar; C: Control; CRBLM: Cerebellum; Dep: Depression; DLPC: Dorsolateral prefrontal cortex; DMP: Differentially methylated probe; EBV: Epstein–Barr virus; FC: Frontal cortex; LCL: Lymphoblastoid cell line; N-A: Native American; NA: Not available; NP: Not published; PVCA: Principal variance component analysis; SZ: Schizophrenia; T: A transformed prostate cancer cell line, primary cell culture of prostate epithelial cell, patient-matched cancer associated fibroblast, nonmalignant tissue associated fibroblast and infant blood from archival guthrie card; TRP: Technical replicate pairs.