Mouse SCN — time-restricted Western-diet feeding
Mus musculus · Suprachiasmatic nucleus · bulk RNA-seq
Selected data and study scope
This dataset contains bulk RNA-seq data from Mus musculus, sampled from suprachiasmatic nucleus. The default comparison examines gene expression in Nine-hour time-restricted Western diet relative to Western diet ad libitum.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Suprachiasmatic nucleus, includes 23 Western diet ad libitum samples and 22 Nine-hour time-restricted Western diet 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. Mouse SCN — time-restricted Western-diet feeding; all 1 registered contrasts on default track scn
Experimental design review needed. Mouse SCN — time-restricted Western-diet feeding; all 1 registered contrasts on default track scn
Author concordance review needed. Matched gene effects; trf_vs_ad_libitum_zt_adjusted. 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
Suprachiasmatic-nucleus RNA-seq from a 24-hour, two-hour-resolution time course comparing 22 Western-diet time-restricted-feeding with 23 isocaloric ad-libitum libraries. Collection ZT is modeled additively and other tissues are excluded (PMID 36599299; GSE190389)
Source publication
Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.
Deota S, Lin T, Chaix A, Williams A, Le H, Calligaro H, et al.
Cell metabolism · 2023
Repository study title
Diurnal transcriptome landscape of a multi-tissue response to time restricted feeding 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
Nine-hour time-restricted Western diet vs Western diet ad libitum · 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 | Western diet ad libitum n | Nine-hour time-restricted Western diet n |
|---|---|---|---|
| Suprachiasmatic nucleus | 16,997 | 23 | 22 |
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.