Table 1.
Sample analyzed and experimental design⁎
| Main experiment | Species | Tissue | Type of storage | Length of storage | Replicates | Histone analyzed | Histone isolation protocol | Super-SILAC spike in |
|---|---|---|---|---|---|---|---|---|
| Experiment #1: fresh-frozen and FFPE mouse samples | mouse | spleen | frozen | few weeks | 2 biological | H3, H4 | #1 | no |
| FFPE | 2 biological | #3 | no | |||||
| liver | frozen | few weeks | 2 technical | #1 | no | |||
| FFPE | 2 technical | #3 | no | |||||
| spleen | frozen | 6 years | 2 technical | #1 | no | |||
| FFPE | 2 technical | #3 | no | |||||
| Experiment #2: fresh-frozen and FFPE human breast cancer biopsies | human | breast cancer (biopsy #1) | frozen | few months | 3 technical | H3 | #2 | yes |
| FFPE | 3 technical | #3 | yes | |||||
| breast cancer (biopsy #2) | frozen | 3 technical | #2 | yes | ||||
| FFPE | 3 technical | #3 | yes | |||||
| breast cancer (biopsy #3) | frozen | 3 technical | #2 | yes | ||||
| FFPE | 3 technical | #3 | yes | |||||
| Experiment #3: FFPE human breast cancer biopsies belonging to different subtypes | human | breast cancer - Luminal A | FFPE | few months | 5 patients | H3 | #3 | yes |
| breast cancer - Luminal B | FFPE | 5 patients | #3 | yes | ||||
| breast cancer - Triple Negative | FFPE | 5 patients | #3 | yes | ||||
| breast cancer - HER2 positive | FFPE | 5 patients | #3 | yes |
⁎
see Table S1 for related raw files.