Cattle hypothalamus — early-life plane of nutrition
Bos taurus · Whole hypothalamus · bulk RNA-seq
Selected data and study scope
This dataset contains bulk RNA-seq data from Bos taurus, sampled from whole hypothalamus. The default comparison examines gene expression in High plane of nutrition relative to Moderate plane of nutrition.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, Remaining hypothalamus, includes 15 Moderate plane of nutrition samples and 14 High plane of nutrition 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 use log2(TMM-normalized count abundance + 1). Keep this unit when exporting or comparing values. Values on other normalization scales are not directly interchangeable.
Evidence and verification
Pipeline QC passed. Cattle hypothalamus — early-life plane of nutrition; all 1 registered contrasts on default track hypothalamus
Experimental design review needed. Cattle hypothalamus — early-life plane of nutrition; all 1 registered contrasts on default track hypothalamus
Author concordance review needed. Selected author genes only; high_vs_moderate_plane_nutrition. P values and FDR are contextual. Numerical acceptance: 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
Remaining-hypothalamus RNA-seq comparing 14 high-plane with 15 moderate-plane early-life nutrition heifer calves. The official author-normalized fractional count-abundance matrix is symbol-collapsed on the linear scale and transformed exactly as log2(x+1) for limma (PMID 34234169; GSE153495)
Source publication
A high plane of nutrition during early life alters the hypothalamic transcriptome of heifer calves.
Sánchez JM, Keogh K, Kelly AK, Byrne CJ, Lonergan P, Kenny DA
Scientific reports · 2021
Repository study title
Effect of early-life plane of nutrition on the transcriptional profile of the hypothalamus in heifer calves
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
High plane of nutrition vs Moderate plane of nutrition · 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 | Moderate plane of nutrition n | High plane of nutrition n |
|---|---|---|---|
| Remaining hypothalamus | 15,634 | 15 | 14 |
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.