Table 2 Data sets for the four main case studies
Study | data set | Summary | Microarray platform | # Of samples | Stages of differentiation/development | # Of probes |
|---|---|---|---|---|---|---|
Kolle et al.52 | GSE13201 | HES2 embryonic stem cells were sorted by the presence of GCTM-2 and CD9 into four populations using Fluorescence Activated Cell Sorting (FACS) method | Illumina Human-6 v2.0 Expression BeadChip (Illumina Inc., San Diego, CA, USA) | 12 | P7 (×3) | 48,687 |
|  |  |  |  |  | P6 (×3) |  |
|  |  |  |  |  | P5 (×3) |  |
|  |  |  |  |  | P4 (×3) |  |
Hartl et al.43 | GSE8091 | Transcriptome of embryonic mouse brain development at 9.5, 11.5 and 13.5 embryonic days | Affymetrix Mouse Genome 430 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA) | 16 | E9 (×6) | 45,102 |
|  |  |  |  |  | E11 (×4) |  |
|  |  |  |  |  | E13 (×6) |  |
Kouno et al.53 | THP1-Mac | Temporal gene-expression changes of THP1 single cells differentiating to macrophages | BioMark Dynamic Arrays of Fluidigm for single-cell (Fluidigm Corporation, San Francisco, CA, USA) | 240 | 0 h (×60) | 45 |
|  |  |  |  |  | 1 h (×60) |  |
|  |  |  |  |  | 6 h (×60) |  |
|  |  |  |  |  | 96 h (×60) |  |
Sartor et al.54 | GSE17708 | Temporal gene-expression changes during TGF-β-induced epithelial-mesenchymal transition | Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix Inc.) | 15 | 0 h (×3) | 54,675 |
|  |  |  |  |  | 8 h (×3) |  |
|  |  |  |  |  | 16 h (×3) |  |
|  |  |  |  |  | 24 h (×3) |  |
|  |  |  |  |  | 72 h (×3) |  |
