Table 1.
Comparison of Experiment Set 2 to other experiments from our group and to all available Jurkat T Cell transcriptome data sets from GEO that are not transfections or knock downs. The utilized data sets were the regular, spliced, and unspliced transcriptome of the Experiment Set 2 data (rRNA depletion sequencing); the previous Experiment Set 1 study with 9 g for 3 min and 15 min (polyA sequencing); the internal centrifugation study with centrifugation at 300× g for 5 min in a standard benchtop centrifuge with different waiting times before RNA isolation after centrifugation, and a 5 min 42 °C heat stress data set; and external GEO data sets with accession number and treatment description. Application period of effects is given. Number of differentially expressed genes, both upregulated and downregulated, is given, based on a false discovery rate-adjusted p value below 0.05 and no fold change cutoff. Number of up- and downregulated genes is also visualized by bar charts, red for upregulated and blue for downregulated genes. Next, the correlation with hypg20s and hypg60 from Experiment Set 2 regular transcriptome is given, based on how many more of the significantly upregulated (up) or downregulated (down) genes of the smaller group were contained in the larger group, than expected. 1 indicates perfect match with the null hypothesis, that any overlaps between upregulated genes or downregulated genes could be explained by random drawing, much smaller than 1 indicates that much less genes were regulated continuously than expected (color-coded in violet), much larger indicates much more (color-coded in cyan). The columns’ 3D distribution indicates how many µm the average distribution of upregulated/downregulated genes deviated from expectation, based on the methodology from Figure 2. Deviation towards the nuclear center are indicated in green, deviation towards the periphery in yellow.
| Sample Name | Treatment | Effect Time | # of Differential Genes | Correlation—Up | Correlation—Down | 3D Distribution | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Up | Down | Total | hypg20s | hypg60 | hypg20s | hypg60 | Up | Down | ||||
| Exp. Set 2 | hypg20s | Centrifugation 9× g | 20 s | 962 | 753 | 1715 | 3.0 | 2.7 | −0.29 | 0.48 | ||
| hypg75s | Centrifugation 9× g | 75 s | 2096 | 1830 | 3926 | 6.0 | 3.8 | 6.0 | 3.8 | −0.33 | 0.40 | |
| hypg3 | Centrifugation 9× g | 3 min | 3001 | 3442 | 6443 | 3.9 | 3.1 | 3.4 | 3.4 | −0.34 | 0.34 | |
| hypg5 | Centrifugation 9× g | 5 min | 896 | 535 | 1431 | 6.7 | 4.4 | 5.7 | 4.2 | −0.31 | 0.24 | |
| hypg7 | Centrifugation 9× g | 7 min | 1021 | 1018 | 2039 | 4.8 | 4.6 | 2.3 | 4.6 | −0.26 | 0.02 | |
| hypg9 | Centrifugation 9× g | 9 min | 1470 | 1164 | 2634 | 3.9 | 4.6 | 3.6 | 4.8 | −0.27 | 0.16 | |
| hypg15 | Centrifugation 9× g | 15 min | 4191 | 4537 | 8728 | 2.2 | 3.2 | 2.6 | 3.4 | −0.35 | 0.32 | |
| hypg60 | Centrifugation 9× g | 60 min | 3704 | 3295 | 6999 | 3.0 | 2.7 | −0.27 | 0.21 | |||
| Ctrl60-Ctrl | Centrifugation 9× g | (60 min) | 4 | 7 | 11 | |||||||
| Exp. Set 2 spliced | hypg20s | Centrifugation 9× g | 20 s | 373 | 253 | 626 | 12.6 | 3.6 | 15.5 | 2.6 | −0.36 | 0.27 |
| hypg75s | Centrifugation 9× g | 75 s | 657 | 1753 | 2410 | 8.6 | 4.1 | 4.2 | 3.1 | −0.43 | 0.15 | |
| hypg3 | Centrifugation 9× g | 3 min | 963 | 2767 | 3730 | 6.8 | 3.8 | 3.1 | 2.7 | −0.45 | 0.17 | |
| hypg5 | Centrifugation 9× g | 5 min | 243 | 943 | 1186 | 8.2 | 4.3 | 3.5 | 3.1 | −0.39 | 0.01 | |
| hypg7 | Centrifugation 9× g | 7 min | 290 | 1983 | 2273 | 6.7 | 4.1 | 1.5 | 2.7 | −0.36 | −0.17 | |
| hypg9 | Centrifugation 9× g | 9 min | 500 | 2541 | 3041 | 4.2 | 3.7 | 2.0 | 2.8 | −0.34 | −0.09 | |
| hypg15 | Centrifugation 9× g | 15 min | 1323 | 6353 | 7676 | 2.7 | 3.4 | 2.0 | 2.4 | −0.47 | 0.22 | |
| hypg60 | Centrifugation 9× g | 60 min | 1855 | 5012 | 6867 | 3.7 | 4.7 | 1.7 | 2.8 | −0.33 | −0.06 | |
| Ctrl60-Ctrl | Centrifugation 9× g | (60 min) | 1 | 7 | 8 | |||||||
| Exp. Set 2 unspliced | hypg20s | Centrifugation 9× g | 20 s | 252 | 60 | 312 | 3.4 | 2.1 | −0.42 | 0.06 | ||
| hypg75s | Centrifugation 9× g | 75 s | 2440 | 286 | 2726 | 2.4 | 2.1 | 3.3 | 2.5 | −0.47 | 0.18 | |
| hypg3 | Centrifugation 9× g | 3 min | 3028 | 766 | 3794 | 2.1 | 1.8 | 2.5 | 2.2 | −0.47 | 0.12 | |
| hypg5 | Centrifugation 9× g | 5 min | 1629 | 93 | 1722 | 2.5 | 2.1 | 2.2 | −0.39 | 0.07 | ||
| hypg7 | Centrifugation 9× g | 7 min | 2314 | 222 | 2536 | 2.2 | 2.0 | 0.9 | 1.4 | −0.34 | −0.06 | |
| hypg9 | Centrifugation 9× g | 9 min | 3599 | 294 | 3893 | 2.1 | 2.0 | 1.0 | 1.4 | −0.37 | −0.04 | |
| hypg15 | Centrifugation 9× g | 15 min | 5282 | 1580 | 6862 | 1.9 | 1.8 | 2.4 | 2.1 | −0.43 | 0.40 | |
| hypg60 | Centrifugation 9× g | 60 min | 5911 | 1147 | 7058 | 1.9 | 2.1 | 1.9 | 2.3 | −0.35 | 0.07 | |
| Ctrl60-Ctrl | Centrifugation 9× g | (60 min) | 0 | 0 | 0 | |||||||
| Exp. Set 1 | hypg3 | Centrifugation 9× g | 3 min | 2464 | 2593 | 5057 | 0.6 | 1.2 | 0.1 | 1.2 | 0.20 | −0.27 |
| hypg15 | Centrifugation 9× g | 15 min | 1844 | 3230 | 5074 | 3.3 | 2.3 | 3.0 | 2.0 | −0.30 | 0.42 | |
| 300 g 5 min | wait 1 min | Centrifugation 300× g | 5 min + 1 min | 8043 | 7030 | 15,073 | 0.2 | 0.8 | 0.2 | 1.4 | 0.28 | −0.27 |
| wait 4 min | Centrifugation 300× g | 5 min + 4 min | 7906 | 7020 | 14,926 | 0.2 | 0.8 | 0.2 | 1.4 | 0.27 | −0.26 | |
| wait 15 min | Centrifugation 300× g | 5 min + 15 min | 8100 | 7130 | 15,230 | 0.2 | 0.8 | 0.2 | 1.4 | 0.27 | −0.25 | |
| wait 15 min–wait 1 min | Centrifugation 300× g | 5 min + 15 min | 15 | 56 | 71 | 0.01 | ||||||
| heat | 42 °C | 5 min | 1279 | 3719 | 4998 | 0.7 | 3.5 | 1.1 | 2.0 | −0.21 | 0.00 | |
| External GEO reference data sets | GSE138290 | 2 mM H2O2 | 30 min | 1023 | 46 | 1069 | 0.7 | 1.3 | −0.02 | |||
| GSE145453 | anti CD3/CD28 antibodies | 2 h | 1081 | 663 | 1744 | 1.7 | 1.0 | 0.6 | 0.8 | −0.03 | −0.16 | |
| GSE145453 | +100 ng/mL chemokines CXCL12 & CCL19 | 2 h | 981 | 506 | 1487 | 2.1 | 1.2 | 0.9 | 1.0 | −0.08 | −0.07 | |
| GSE85201 | activation with 50 mM PMA + 1 µM Ionomycin | 5 min | 405 | 379 | 784 | 1.0 | 1.7 | 0.5 | 1.1 | −0.02 | −0.14 | |
| GSE174380 | 100 IU/mL Interferon IFNb | 4 h | 246 | 391 | 637 | 0.8 | 1.1 | 2.8 | 1.5 | −0.04 | 0.46 | |
| GSE174380 | 100 IU/mL Interferon IFNb | 8 h | 359 | 98 | 457 | 0.7 | 0.9 | 1.0 | 1.2 | 0.05 | −0.01 | |
| GSE174380 | 100 IU/mL Interferon IFNb | 12 h | 347 | 204 | 551 | 0.9 | 1.3 | 1.7 | 1.8 | 0.02 | −0.01 | |
| GSE93594 | 20 ng/mL phorbol ester PMA | 48 h | 5840 | 5779 | 11,619 | 1.3 | 1.3 | 1.3 | 1.9 | −0.03 | −0.03 | |
| GSE166630 | pEF-GFP transfection with Lipofectamine LTX | 24 h | 68 | 88 | 156 | 1.1 | 0.7 | 4.8 | 1.4 | −0.36 | 0.60 | |
| GSE134401 | NOTCH inhibition with CB-103 | 8 h | 571 | 397 | 968 | 1.2 | 1.0 | 1.3 | 1.5 | 0.03 | −0.02 | |
| GSE134401 | NOTCH inhibition with DAPT | 8 h | 17 | 29 | 46 | |||||||
| GSE134401 | NOTCH inhibition with RIN1 | 8 h | 796 | 644 | 1440 | 0.9 | 1.7 | 1.9 | 1.4 | −0.17 | 0.12 | |
| GSE134401 | NOTCH inhibition with siRBPJ | 48 h | 0 | 3 | 3 | |||||||
| GSE120612 | 10 µM topoisomerase II inhibitor etoposide | 4 h | 5090 | 4656 | 9746 | 1.4 | 1.7 | 1.3 | 1.5 | −0.08 | 0.08 | |
| GSE160349 | 2 µM NOTCH inhibitor Chidamide | 48 h | 5802 | 4785 | 10,587 | 1.3 | 1.0 | 1.1 | 1.9 | 0.00 | −0.05 | |
| GSE182659 | 1 µM CDK4/6 inhibitor Palbociclib | 72 h | 2512 | 2476 | 4988 | 1.1 | 1.0 | 1.0 | 1.3 | −0.07 | −0.02 | |
| GSE139621 | 30 nM splicing modulator H3B8800 | 6 h | 7173 | 6674 | 13,847 | 1.7 | 1.5 | 1.3 | 1.4 | −0.13 | 0.05 | |
| GSE139621 | 30 nM splicing modulator H3B8800 | 24 h | 4878 | 5054 | 9932 | 1.8 | 1.5 | 1.3 | 1.7 | −0.08 | 0.02 | |
| GSE139621 | 10 µM Ubiquitin-spec. prot. 7 inhibitor P5091 | 24 h | 6356 | 5606 | 11,962 | 1.1 | 0.8 | 0.8 | 0.9 | 0.04 | −0.10 | |
| GSE97435 | 1 µM NOTCH inhibitor GSI | 24 h | 347 | 351 | 698 | 1.8 | 1.1 | 1.3 | 1.7 | 0.03 | 0.03 | |
| GSE97435 | 500 nM BRD4 histone acetylase inhibitor JQ1 | 24 h | 4291 | 5145 | 9436 | 1.0 | 1.0 | 0.7 | 1.2 | 0.07 | −0.11 | |