Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon
Bibliographic record
Abstract
Abstract The circadian clock is a molecular timer present throughout the body, including the gastrointestinal tract, where it regulates daily rhythms in physiology through the timing of rhythmic gene expression. Dysfunctional rhythms, caused by loss of clock timing and/or environmental disruption is implicated with gastrointestinal dysfunction and pathology. The large intestine (colon) is composed of many different types of cells with distinct gene expression programs and functions. How daily rhythms in transcript abundance are coordinated in the intestine at a cell-specific level is not known. Using single cell transcriptomics, we analyzed 24-hour gene expression in all major cell types of the proximal and distal regions of the colon following injury. We find that daily gene expression is not uniform: rhythmic genes, including circadian clock components, clock targets, and systemic programs, differ in their timing and are cell-type specific. Cells of the epithelium, stroma, and immune system to display strong rhythms in metabolic, protein processing, and stress response genes during regeneration. While stromal and muscle cells exhibit robust circadian clock gene rhythms irrespective of injury, epithelial cells show weaker clock oscillations that become 12-hours antiphasic during regeneration. These data, completed with smFISH validation, reveal an unexpected complexity to daily transcript levels in the colon, and provide a resource for future studies by identifying the cellular source of 24-hour transcript rhythms.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
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".