Table 1.
Summary of ChIP conditions and bioinformatics treatment for each experiment (NR = not relevant, NA = not available)
| ChIP antibodies and conditions used (* For ChIP-QPCR) | Peak detection | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Experiment | Antibody (clone) | Origin | Reference Antibody | Number of cells | Antibody/Beads | Washes (RIPA/TE) | Replicates Number | Tags Not Aligned/Multiple Alignment (× 106) | Tags Used (× 106) | Lanes Number | Extension Size (bp) | Threshold | Max Gap |
| Pol II | Total (N-20) | Rabbit polyclonal | Santa Cruz (sc-899x) | 1 × 108 | 20 µg/200 µl | 8x/1x | 1 | 8.93 | 19.83 | 1 | 176 | 80 | 350 |
| 2 | 17.94 | 33.02 | 2 | 166 | |||||||||
| 3 | 16.54 | 28.48 | 1 | 156 | |||||||||
| H3K4me1 | H3K4me1 | Rabbit polyclonal | Abcam (ab8895) | 5 × 106 | 2 µg/20 µl | 8x/1x | 1 | 9.35 | 7.83 | 1 | 176 | 60 | 700 |
| 2 | 7.59 | 20.93 | 1 | 226 | |||||||||
| H3K4me3 | H3K4me3 | Rabbit polyclonal | Abcam (ab8580) | 5 × 106 | 2 µg/20 µl | 8x/1x | 1 | 7.12 | 2.61 | 1 | 186 | 50 | 400 |
| 2 | NA | 14.14 | 1 | 123 | |||||||||
| H3K36me3 | H3K36me3 | Rabbit polyclonal | Abcam (ab9050) | 2 × 107 | 8 µg/80 µl | 8x/1x | 1 | NA | 21.21 | 1 | 196 | 40 | 1000 |
| 2 | NA | 5.57 | 1 | 316 | |||||||||
| H3K27ac | H3K27ac | Rabbit polyclonal | Ab4729 | 5 × 106 | 2 µg/20 µl | 5x/1x | 1 | 5.33 | 52.50 | 1 | 197 | 100 | 750 |
| Tyr1P | Tyr1P (3D12) | Rat monoclonal | Mayer et al. (2012) | 1 × 108 | 10 µg/100 µl | 5x/1x | 1 | 12.30 | 15.56 | 1 | 206 | NR | NR |
| 2 | 9.98 | 15.55 | 1 | 276 | |||||||||
| Tyr1P (8G5) | Rat monoclonal | This article | 1 × 108 | 10 µg/100 µl | 5x/1x | 1 | 30.26 | 28.78 | 1 | 187 | NR | NR | |
| Ser2P | Ser2P (3E10) | Rat monoclonal | Chapman et al. (2007) | 2 × 108 | 80 µg/400 µl | 5x/1x | 1 | 9.31 | 11.28 | 1 | 192 | NR | NR |
| 2 | 9.85 | 15.94 | 1 | 286 | |||||||||
| Ser5P | Ser5P (3E8) | Rat monoclonal | Chapman et al. (2007) | 1.2 × 108 (2.5 × 107*) | 24 µg/240 µl (5 µg/50 µl*) | 8x/1x | 1 | NA | 13.98 | 1 | 146 | NR | NR |
| 2 | NA | 3.57 | 1 | 216 | |||||||||
| Ser7P | Ser7P (4E12) | Rat monoclonal | Chapman et al. (2007) | 1 × 108 | 10 µg/100 µl | 5x/1x | 1 | NA | 16.46 | 1 | 156 | NR | NR |
| 2 | NA | 1.92 | 1 | 226 | |||||||||
| Short-RNA-seq | NR | NR | NR | 1 × 107 | NR | NR | 1 | NA | 9.87 | 1 | NR | NR | NR |
| MNase-seq | NR | NR | NR | 2 × 107 | NR | NR | 1 | 90.00 | 289.60 | 1 | 152/NR midpoints** | NR | NR |
| Input | NR | NR | NR | NR | NR | NR | 1 | 20.10 | 18.18 | 1 | 126 | NR | NR |
| 2 | NA | 29.74 | 1 | 146 | |||||||||
| 3 | 15.41 | 24.93 | 1 | 118 | |||||||||
| 4 | 11.20 | 28.32 | 1 | 196 | |||||||||
**
For MNase-seq, the experiment was performed and processed in pair-end. For nucleosome density, tags were not elongated but connected and the indicated sequence average length is withdrawn by our analysis pipeline using the pair-end information. For midpoints analyses, elongation does not apply and data treatment is indicated earlier in ‘Materials and methods–Processing of sequenced tags’.