Additional file 1 of Distinct roles of histone H2B ubiquitination at promoters and coding regions of Pol II-transcribed stress genes
Bibliographic record
Abstract
Additional file 1: Fig. S1. Ubp8 or Ubp16 depletion confers long-lived phenotypes depending on Atf1 activity. Fig. S2. Alternative strategies to generate Ubp8 or Ubp16 depleted cells. Fig. S3-S4. Transcriptome landscape of DUB mutants showed up-regulated stress response. Fig. S5. ChIP-seq analysis of Rbp1-HA (Pol II) and phosphorylated Pol II at Ser2. Fig. S6. Mutations of H2B ubiquitination regulators affect tolerance to oxidative stress. Fig. S7. ChIP-seq analysis of Ubp8 and Ubp16. Fig. S8. Nucleosome eviction upon H2O2 treatment is more sustained in cells lacking DUBs. Fig. S9. Genetic interactions of H2Bub with chromatin remodelers, FACT, SAGA or COMPASS. Fig. S10. Chromatin remodelers, and histone marks writers genetically interact with DUBs function.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.012 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.863 | 0.220 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".