Djungarian-hamster hypothalamus — spontaneous daily torpor
Phodopus sungorus · Whole hypothalamus · bulk RNA-seq
Selected data and study scope
This dataset contains bulk RNA-seq data from Phodopus sungorus, sampled from whole hypothalamus. The default comparison examines gene expression in Short-photoperiod spontaneous torpor relative to Short-photoperiod normothermia.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Whole hypothalamus, includes 4 Short-photoperiod normothermia samples and 4 Short-photoperiod spontaneous torpor 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. Djungarian-hamster hypothalamus — spontaneous daily torpor; all 1 registered contrasts on default track hypothalamus
Experimental design passed. Djungarian-hamster hypothalamus — spontaneous daily torpor; all 1 registered contrasts on default track hypothalamus
Author concordance review needed. Selected author genes only; spontaneous_torpor_vs_normothermia_author_mouse_projection. P values and FDR are contextual. No numerical acceptance route has passed for this scope.
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
Whole-hypothalamus RNA-seq at ZT04 comparing four short-photoperiod hamsters in spontaneous daily torpor with four short-photoperiod normothermic animals, adjusted for sex. Long-photoperiod animals are excluded; fractional RSEM count estimates are keyed by the authors' documented BLASTx projection to mouse GRCm39 GeneIDs and preserved without rounding (PMID 34894101; GSE179663)
Source publication
Haugg E, Borner J, Diedrich V, Herwig A
FEBS open bio · 2022
Repository study title
Transcriptomics of the Djungarian Hamster Hypothalamus
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Short-photoperiod spontaneous torpor vs Short-photoperiod normothermia · 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 | Short-photoperiod normothermia n | Short-photoperiod spontaneous torpor n |
|---|---|---|---|
| Whole hypothalamus | 15,099 | 4 | 4 |
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.