Mouse whole hypothalamus — 24-hour food deprivation (scRNA-seq)
Mus musculus · Whole hypothalamus · scRNA-seq
Selected data and study scope
This dataset contains scRNA-seq data from Mus musculus, sampled from whole hypothalamus. The default comparison examines gene expression in Food deprived (24 h) relative to Normal fed.
The explorer includes 1 track and 1 comparison for this dataset. One comparison is marked exploratory because it was not run in the source study.
The default track, Whole hypothalamus (mouse pseudobulk), includes 4 Normal fed samples and 3 Food deprived (24 h) samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
The source assay profiles individual cells. The track and sample counts shown here describe the analysis used for the comparison. Cell counts do not replace independent biological replicates.
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 review needed. Mouse whole hypothalamus — 24-hour food deprivation (scRNA-seq); all 1 registered contrasts on default track hypothalamus
Experimental design review needed. Mouse whole hypothalamus — 24-hour food deprivation (scRNA-seq); all 1 registered contrasts on default track hypothalamus
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
Adult mouse whole-hypothalamus Drop-seq, 17 technical partitions (18,300 cells) resolved to seven author-defined processed units, normal fed n=4 (B0_Normal, B1_Normal, B2_Normal, B3_Normal) vs 24-hour food deprived n=3 (B1_Hungry, B2_Hungry2, B4_Hungry2), with sequencing batch modeled; one residual degree of freedom, so the comparison is exploratory: effect sizes and pathway ranks, no gene-level FDR calls (Chen et al., Cell Rep 2017, PMID 28355573; GSE87544)
Source publication
Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity.
Chen R, Wu X, Jiang L, Zhang Y
Cell reports · 2017
Repository study title
Single-cell RNA-seq reveals hypothalamic cell diversity
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Food deprived (24 h) vs Normal fed · default
Exploratory comparison: read effect sizes (logFC) and pathway ranks, not gene-level significance. The edgeR-QL fit models sequencing batch (~ batch + group) on seven processed units, 4 fed vs 3 food-deprived, which leaves one residual degree of freedom; its gene-level p-values and FDR depend on the edgeR version far more than on the data, so no gene-level FDR call is made for this dataset.
This exploratory comparison is a reanalysis. The source study did not run it.
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 | Normal fed n | Food deprived (24 h) n |
|---|---|---|---|
| Whole hypothalamus (mouse pseudobulk) | 14,881 | 4 | 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.