Mouse postnatal hypothalamus — microglia depletion
Mus musculus · Whole hypothalamus · bulk RNA-seq
Selected data and study scope
This dataset contains bulk RNA-seq data from Mus musculus, sampled from whole hypothalamus. The default comparison examines gene expression in PLX3397 P9-P15 relative to Vehicle P9-P15.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Whole hypothalamus, includes 4 Vehicle P9-P15 samples and 4 PLX3397 P9-P15 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 postnatal hypothalamus — microglia depletion; all 1 registered contrasts on default track hypothalamus
Experimental design review needed. Mouse postnatal hypothalamus — microglia depletion; 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
P19 whole-hypothalamus RNA-seq comparing four PLX3397-treated neonatal profiles with four vehicle controls after P9-P15 gavage. Each arm contains two female and two male profiles and sex is modeled additively; library-to-litter and within-litter treatment allocation remain unresolved (PMID 38001338; GSE243697)
Source publication
Microglia shape AgRP neuron postnatal development via regulating perineuronal net plasticity.
Sun J, Wang X, Sun R, Xiao X, Wang Y, Peng Y, et al.
Molecular psychiatry · 2024
Repository study title
Microglia shape AgRP neuron postnatal development via regulating perineuronal net plasticity
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
PLX3397 P9-P15 vs Vehicle P9-P15 · 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 | Vehicle P9-P15 n | PLX3397 P9-P15 n |
|---|---|---|---|
| Whole hypothalamus | 21,884 | 4 | 4 |
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.