Mouse SCN — chow vs high-fat diet (bulk RNA-seq)
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 High-fat diet relative to Chow.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Suprachiasmatic nucleus (SCN), includes 18 Chow samples and 18 High-fat 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 use a log2-normalized scale. They are not raw counts or CPM. Check this study's preprocessing before comparing them with other datasets.
Evidence and verification
Pipeline QC passed. Mouse SCN — chow vs high-fat diet (bulk RNA-seq); all 1 registered contrasts on default track scn
Experimental design not assessed. Mouse SCN — chow vs high-fat diet (bulk RNA-seq); all 1 registered contrasts on default track scn
Author concordance not assessed. Author effect concordance has not been assessed
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
Reshaping circadian metabolism in the suprachiasmatic nucleus and prefrontal cortex by nutritional challenge — SCN sampled every 4 h across 24 h, chow vs high-fat diet (GSE157077)
Source publication
Tognini P, Samad M, Kinouchi K, Liu Y, Helbling JC, Moisan MP, et al.
Proceedings of the National Academy of Sciences of the United States of America · 2020
Repository study title
Reshaping Circadian Metabolism in the Suprachiasmatic Nucleus and Prefrontal Cortex by Nutritional Challenge
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
High-fat diet vs Chow · default
Time-course design
SCN sampled every 4 h across one 24 h light–dark cycle (ZT0–ZT20), normal chow vs high-fat diet, 3 mice per arm per timepoint. 36 libraries.
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 | Chow n | High-fat diet n |
|---|---|---|---|
| Suprachiasmatic nucleus (SCN) | 14,644 | 18 | 18 |
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.