Siberian-hamster MBH — short photoperiod
Phodopus sungorus · Whole hypothalamus · bulk long-read RNA-seq
Selected data and study scope
This dataset contains bulk long-read RNA-seq data from Phodopus sungorus, sampled from whole hypothalamus. The default comparison examines gene expression in Four weeks short day relative to Long day.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Mediobasal hypothalamus, includes 6 Long day samples and 6 Four weeks short day samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
The measurement combines expression from the cells in the tissue sample. A difference in tissue expression alone does not identify which cell type contributes to it.
Expression values are CPM (TMM-normalized): counts per million on library sizes adjusted by the TMM factors of the study’s own edgeR fit. This scale adjusts for library size and composition, not gene length. Use it to inspect a feature across the samples in this analysis. CPM values are not absolute transcript counts.
Evidence and verification
Pipeline QC passed. Siberian-hamster MBH — short photoperiod; all 1 registered contrasts on default track mbh
Experimental design review needed. Siberian-hamster MBH — short photoperiod; all 1 registered contrasts on default track mbh
Author concordance review needed. Matched gene effects; four_week_short_day_vs_long_day_author_mouse_projection. P values and FDR are contextual. Numerical acceptance: strong correlation and matched-gene direction.
Pipeline QC can pass while experimental-design limitations remain. Read both assessments before interpreting results.
Open the dataset in the Explorer to read each check and its evidence. Author concordance compares effects for matched genes. It does not require identical author P values or FDR.
Read the analysis methods and interpretation guide and how to cite the source study and HypoExplorer. The source publication may include tissues, groups or comparisons beyond the data shown here.
Source study
Mediobasal-hypothalamus Oxford Nanopore RNA-seq comparing six hamsters after four weeks of short day with six long-day controls. Pituitary and other hypothalamic regions/time points are excluded; fractional Salmon estimates are summed without rounding using the authors' explicit alignment to mouse GRCm39 (PMID 41527434; GSE274003)
Source publication
Hypothalamic deiodinase type-3 establishes the period of circannual interval timing in mammals.
Stewart C, Liddle TA, Tolla E, Lewis JE, Marshall C, Evans NP, et al.
eLife · 2026
Repository study title
Deiodinase type-3 establishes the period of circannual interval timing in mammals
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Four weeks short day vs Long day · default
Positive differential-expression values indicate higher expression in the case group relative to the baseline. Check the comparison direction and study design when interpreting results.
Available tracks
| Track | Features | Long day n | Four weeks short day n |
|---|---|---|---|
| Mediobasal hypothalamus | 6,671 | 6 | 6 |
Expression and analysis results
Open this dataset to inspect gene expression and differential-expression results across the available tracks. Pathway enrichment is also available. The pathway databases differ by dataset.
HypoExplorer is in beta testing. Features and analyses may change during testing. Review the original source, analysis methods and quality-control checks before using a result in research.