Mouse SCN NPAS4 and light response
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 NPAS4 knockout, dark relative to Wild type, dark.
The explorer includes 1 track and 4 comparisons for this dataset.
The default track, Suprachiasmatic nucleus, includes 3 Wild type, dark samples and 3 NPAS4 knockout, dark 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 NPAS4 and light response; all 1 registered tracks and 4 comparisons
Experimental design review needed. Mouse SCN NPAS4 and light response; all 1 registered tracks and 4 comparisons
Author concordance review needed. All 1 track(s) and 4 separately measured comparison(s). ko_vs_wt_dark: Matched gene effects; ko_vs_wt_dark. P values and FDR are contextual. Numerical acceptance: matched-gene direction. ko_vs_wt_light: Matched gene effects; ko_vs_wt_light. P values and FDR are contextual. Numerical acceptance: matched-gene direction. light_vs_dark_wt: Matched gene effects; light_vs_dark_wt. P values and FDR are contextual. Numerical acceptance: strong correlation and matched-gene direction. light_vs_dark_ko: Matched gene effects; light_vs_dark_ko. P values and FDR are contextual. Numerical acceptance: 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
NPAS4 bulk experiment only. Each genotype/light arm has three independent pools of six SCN pairs. Time-course and ChIP assays are separate experiments and excluded.
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Knockout vs wild type in dark · default
Knockout vs wild type after light
Light vs dark in wild type
Light vs dark in knockout
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 | Wild type, dark n | NPAS4 knockout, dark n |
|---|---|---|---|
| Suprachiasmatic nucleus | 14,793 | 3 | 3 |
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.