Mouse hypothalamus — 23 vs 4 months (spatial RNA-seq)
Mus musculus · Whole hypothalamus · spatial RNA-seq
Selected data and study scope
This dataset contains spatial RNA-seq data from Mus musculus, sampled from whole hypothalamus. The default comparison examines gene expression in Aged (23 months) relative to Young (4 months).
For each independent female mouse, the analysis aggregates hypothalamic spatial profiles from sections 4 and 5. It compares 23 months with 4 months of age.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Hypothalamus (spatial animal pseudobulk), includes 3 Young (4 months) samples and 3 Aged (23 months) samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
This reanalysis uses the deposited 2024 cohort of 128,405 profiles. It is not the final publication's revised 98,006-profile cohort. Individual spatial profiles are not independent animal replicates.
The source assay measures spatial profiles. Before interpreting sample counts or differential expression, check how profiles and sections are grouped into analysis samples.
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 hypothalamus — 23 vs 4 months (spatial RNA-seq); all 1 registered contrasts on default track hypothalamus
Experimental design passed. Mouse hypothalamus — 23 vs 4 months (spatial RNA-seq); all 1 registered contrasts on default track hypothalamus
Author concordance review needed. Selected author genes only; aged_vs_young. P values and FDR are contextual. Numerical acceptance: strong correlation and 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
Female mouse brain IRISeq, hypothalamic spots from sections 4 and 5 aggregated to independent animals, 4 months n=3 vs 23 months n=3. Independent reanalysis of the deposited 2024 128,405-profile cohort, not the final paper's revised 98,006-profile cohort (Abdulraouf et al., Nat Neurosci 2026, PMID 42120609; GSE270383)
Source publication
Optics-free spatial genomics for mapping mammalian brain aging by IRISeq.
Abdulraouf A, Jiang W, Zhang Z, Xu Z, Lu Z, Merlinsky T, et al.
Nature neuroscience · 2026
Repository study title
Spatial Mapping of Mouse Brain Aging through Indexed Sequencing
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Aged (23 months) vs Young (4 months) · 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 | Young (4 months) n | Aged (23 months) n |
|---|---|---|---|
| Hypothalamus (spatial animal pseudobulk) | 12,337 | 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.