Mouse P22 hypothalamus — Lef1 conditional knockout
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 P22 Lef1 conditional knockout relative to P22 Lef1 control.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, P22 whole hypothalamus, includes 3 P22 Lef1 control samples and 3 P22 Lef1 conditional knockout 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 P22 hypothalamus — Lef1 conditional knockout; all 1 registered contrasts on default track hypothalamus
Experimental design passed. Mouse P22 hypothalamus — Lef1 conditional knockout; all 1 registered contrasts on default track hypothalamus
Author concordance passed. Matched gene effects; lef1_cko_vs_control_p22. 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
P22 whole-hypothalamus RNA-seq from three Nkx2-1Cre/+;Lef1flox/+ controls and three Nkx2-1Cre/+;Lef1flox/flox conditional-knockout littermates, with unique GSM, BioSample, and SRA experiment identifiers. The zebrafish and embryonic-mouse arms are excluded from this mature-mouse contrast (PMID 28837622; GSE98519)
Source publication
Lef1-dependent hypothalamic neurogenesis inhibits anxiety.
Xie Y, Kaufmann D, Moulton MJ, Panahi S, Gaynes JA, Watters HN, et al.
PLoS biology · 2017
Repository study title
Identification of Lef1-dependent genes in zebrafish and mouse hypothalamus
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
P22 Lef1 conditional knockout vs P22 Lef1 control · 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 | P22 Lef1 control n | P22 Lef1 conditional knockout n |
|---|---|---|---|
| P22 whole hypothalamus | 16,297 | 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.