Mouse SCN — developmental photoperiod
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 Long photoperiod relative to Short photoperiod.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Suprachiasmatic nucleus, includes 9 Short photoperiod samples and 9 Long photoperiod 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 — developmental photoperiod; all 1 registered contrasts on default track scn
Experimental design review needed. Mouse SCN — developmental photoperiod; 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
Whole-SCN RNA-seq from nine male P50 mice entrained to long days from conception versus nine short-day controls, all sampled at projected ZT12 after at least 36 hours in constant darkness. Both balanced sequencing cycles are retained and modeled additively (PMID 39096022; GSE266472)
Source publication
Cox OH, Giannoni-Guzmán MA, Cartailler JP, Cottam MA, McMahon DG
Journal of biological rhythms · 2024
Repository study title
Transcriptomic Plasticity of the Circadian Clock in Response to Photoperiod: A Study in Male Melatonin-Competent Mice
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Long photoperiod vs Short photoperiod · 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 n | Long photoperiod n |
|---|---|---|---|
| Suprachiasmatic nucleus | 18,335 | 9 | 9 |
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.