Mouse GT1-7 hypothalamic neurons — orexin-A response
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 Orexin-A, 3 hours relative to Vehicle, 3 hours.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, GT1-7 hypothalamic neurons, includes 3 Vehicle, 3 hours samples and 3 Orexin-A, 3 hours samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
These data come from a cell-culture model. Check the cell line or differentiation system and the conditions sampled before interpreting a result.
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 GT1-7 hypothalamic neurons — orexin-A response; all 1 registered contrasts on default track gt17
Experimental design passed. Mouse GT1-7 hypothalamic neurons — orexin-A response; all 1 registered contrasts on default track gt17
Author concordance passed. Matched gene effects; orexin_a_3h_vs_vehicle_paired. 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
GT1-7 hypothalamic neuronal cells stably expressing human orexin receptor 1, comparing three 3-hour orexin-A culture preparations with three 8-hour vehicle preparations. Replicate number is included as a blocking factor. Treatment and incubation duration differ; the 8-hour orexin-A profiles are excluded from this contrast (PMID 29145494; GSE99690)
Source publication
Koesema E, Kodadek T
PloS one · 2017
Repository study title
Global Analysis of Gene Expression Mediated By Orexin Receptor 1 Signaling in a Hypothalamic Cell Line
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Orexin-A, 3 hours vs Vehicle, 3 hours · 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, 3 hours n | Orexin-A, 3 hours n |
|---|---|---|---|
| GT1-7 hypothalamic neurons | 15,785 | 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.